diff --git a/src/main/java/org/breedinginsight/api/model/v1/request/SubEntityDatasetRequest.java b/src/main/java/org/breedinginsight/api/model/v1/request/SubEntityDatasetRequest.java
new file mode 100644
index 000000000..c45cfae31
--- /dev/null
+++ b/src/main/java/org/breedinginsight/api/model/v1/request/SubEntityDatasetRequest.java
@@ -0,0 +1,38 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.breedinginsight.api.model.v1.request;
+
+import io.micronaut.core.annotation.Introspected;
+import lombok.*;
+
+import javax.validation.constraints.NotBlank;
+import javax.validation.constraints.NotNull;
+
+@Getter
+@Setter
+@Builder
+@ToString
+@AllArgsConstructor
+@NoArgsConstructor
+@Introspected
+public class SubEntityDatasetRequest {
+    @NotBlank
+    private String name;
+    @NotNull
+    private int repeatedMeasures;
+}
diff --git a/src/main/java/org/breedinginsight/api/v1/controller/ExperimentController.java b/src/main/java/org/breedinginsight/api/v1/controller/ExperimentController.java
index 017197219..77214c9cf 100644
--- a/src/main/java/org/breedinginsight/api/v1/controller/ExperimentController.java
+++ b/src/main/java/org/breedinginsight/api/v1/controller/ExperimentController.java
@@ -9,20 +9,25 @@
 import io.micronaut.security.annotation.Secured;
 import io.micronaut.security.rules.SecurityRule;
 import lombok.extern.slf4j.Slf4j;
+import org.brapi.client.v2.model.exceptions.ApiException;
 import org.breedinginsight.api.auth.ProgramSecured;
 import org.breedinginsight.api.auth.ProgramSecuredRoleGroup;
+import org.breedinginsight.api.model.v1.request.SubEntityDatasetRequest;
 import org.breedinginsight.api.model.v1.response.Response;
 import org.breedinginsight.brapi.v2.model.request.query.ExperimentExportQuery;
 import org.breedinginsight.brapi.v2.services.BrAPITrialService;
 import org.breedinginsight.model.Dataset;
+import org.breedinginsight.model.DatasetMetadata;
 import org.breedinginsight.model.DownloadFile;
 import org.breedinginsight.model.Program;
 import org.breedinginsight.services.ProgramService;
 import org.breedinginsight.services.exceptions.DoesNotExistException;
+import org.breedinginsight.services.exceptions.UnprocessableEntityException;
 import org.breedinginsight.utilities.response.mappers.ExperimentQueryMapper;
 
 import javax.inject.Inject;
 import javax.validation.Valid;
+import java.util.List;
 import java.util.Optional;
 import java.util.UUID;
 
@@ -89,4 +94,57 @@ public HttpResponse<Response<Dataset>> getDatasetData(
         }
     }
 
+    /**
+     * Creates a sub-entity dataset for a given program and experiment with the specified name and number of repeated measures.
+     * @param programId The UUID of the program.
+     * @param experimentId The UUID of the experiment.
+     * @param datasetRequest The POST body, contains the dataset name and number of repeated measures to create.
+     * @return An HttpResponse with a Response object containing the newly created Dataset.
+     */
+    @Post("/${micronaut.bi.api.version}/programs/{programId}/experiments/{experimentId}/dataset")
+    @ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.ALL})
+    @Produces(MediaType.APPLICATION_JSON)
+    public HttpResponse<Response<Dataset>> createSubEntityDataset(
+            @PathVariable("programId") UUID programId,
+            @PathVariable("experimentId") UUID experimentId,
+            @Body @Valid SubEntityDatasetRequest datasetRequest) {
+        try {
+            Optional<Program> programOptional = programService.getById(programId);
+            if (programOptional.isEmpty()) {
+                return HttpResponse.status(HttpStatus.NOT_FOUND, "Program does not exist");
+            }
+
+            Response<Dataset> response = new Response(experimentService.createSubEntityDataset(programOptional.get(), experimentId, datasetRequest));
+            return HttpResponse.ok(response);
+        } catch (Exception e){
+            log.info(e.getMessage());
+            return HttpResponse.status(HttpStatus.UNPROCESSABLE_ENTITY, e.getMessage());
+        }
+    }
+
+    /**
+     * Retrieves the datasets for a given program and experiment.
+     *
+     * @param programId The UUID of the program.
+     * @param experimentId The UUID of the experiment.
+     * @return An HttpResponse with a Response object containing a list of DatasetMetadata.
+     * @throws DoesNotExistException if the program does not exist.
+     * @throws ApiException if an error occurs while retrieving the datasets.
+     */
+    @Get("/${micronaut.bi.api.version}/programs/{programId}/experiments/{experimentId}/datasets")
+    @ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.ALL})
+    @Produces(MediaType.APPLICATION_JSON)
+    public HttpResponse<Response<List<DatasetMetadata>>> getDatasets(
+            @PathVariable("programId") UUID programId,
+            @PathVariable("experimentId") UUID experimentId) throws DoesNotExistException, ApiException {
+
+        Optional<Program> programOptional = programService.getById(programId);
+        if (programOptional.isEmpty()) {
+            return HttpResponse.status(HttpStatus.NOT_FOUND, "Program does not exist");
+        }
+
+        Response<List<DatasetMetadata>> response = new Response(experimentService.getDatasetsMetadata(programOptional.get(), experimentId));
+        return HttpResponse.ok(response);
+
+    }
 }
diff --git a/src/main/java/org/breedinginsight/brapi/v2/constants/BrAPIAdditionalInfoFields.java b/src/main/java/org/breedinginsight/brapi/v2/constants/BrAPIAdditionalInfoFields.java
index 87fbfdda9..6ea30cd20 100644
--- a/src/main/java/org/breedinginsight/brapi/v2/constants/BrAPIAdditionalInfoFields.java
+++ b/src/main/java/org/breedinginsight/brapi/v2/constants/BrAPIAdditionalInfoFields.java
@@ -43,7 +43,9 @@ public final class BrAPIAdditionalInfoFields {
     public static final String EXPERIMENT_NUMBER = "experimentNumber";
     public static final String ENVIRONMENT_NUMBER = "environmentNumber";
     public static final String STUDY_NAME = "studyName";
+    @Deprecated
     public static final String OBSERVATION_DATASET_ID = "observationDatasetId";
+    public static final String DATASETS = "datasets";
     public static final String FEMALE_PARENT_UNKNOWN = "femaleParentUnknown";
     public static final String MALE_PARENT_UNKNOWN = "maleParentUnknown";
 	public static final String TREATMENTS = "treatments";
diff --git a/src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIObservationDAO.java b/src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIObservationDAO.java
index 6eb4c2761..92b45633c 100644
--- a/src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIObservationDAO.java
+++ b/src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIObservationDAO.java
@@ -205,6 +205,24 @@ public List<BrAPIObservation> getObservationsByObservationUnitsAndVariables(Coll
                 .collect(Collectors.toList());
     }
 
+    public List<BrAPIObservation> getObservationsByObservationUnits(Collection<String> ouDbIds, Program program) throws ApiException {
+        if(ouDbIds.isEmpty()) {
+            return Collections.emptyList();
+        }
+        return getProgramObservations(program.getId()).values().stream()
+                .filter(o -> ouDbIds.contains(o.getObservationUnitDbId()))
+                .collect(Collectors.toList());
+    }
+
+    public List<BrAPIObservation> getObservationsByObservationUnitsAndStudies(Collection<String> ouDbIds, Collection<String> studyDbIds, Program program) throws ApiException {
+        if(ouDbIds.isEmpty()) {
+            return Collections.emptyList();
+        }
+        return getProgramObservations(program.getId()).values().stream()
+                .filter(o -> ouDbIds.contains(o.getObservationUnitDbId()) && studyDbIds.contains(o.getStudyDbId()))
+                .collect(Collectors.toList());
+    }
+
     @NotNull
     private ApiResponse<Pair<Optional<BrAPIObservationListResponse>, Optional<BrAPIAcceptedSearchResponse>>> searchObservationsSearchResultsDbIdGet(UUID programId, String searchResultsDbId, Integer page, Integer pageSize) throws ApiException {
         ObservationsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), ObservationsApi.class);
diff --git a/src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIObservationUnitDAO.java b/src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIObservationUnitDAO.java
index 7d8fd9651..aeb919a2f 100644
--- a/src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIObservationUnitDAO.java
+++ b/src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIObservationUnitDAO.java
@@ -170,7 +170,8 @@ public List<BrAPIObservationUnit> getObservationUnitByName(List<String> observat
     }
 
     /**
-     * Create observation units, mutates brAPIObservationUnitList
+     * Create observation units with import progress.
+     * Mutates brAPIObservationUnitList.
      */
     public List<BrAPIObservationUnit> createBrAPIObservationUnits(List<BrAPIObservationUnit> brAPIObservationUnitList, UUID programId, ImportUpload upload) throws ApiException, DoesNotExistException {
         Program program = programService.getById(programId).orElseThrow(() -> new DoesNotExistException("Program id does not exist"));
@@ -190,6 +191,28 @@ public List<BrAPIObservationUnit> createBrAPIObservationUnits(List<BrAPIObservat
         }
     }
 
+    /**
+     * Create observation units without import progress.
+     * Mutates brAPIObservationUnitList.
+     */
+    public List<BrAPIObservationUnit> createBrAPIObservationUnits(List<BrAPIObservationUnit> brAPIObservationUnitList, UUID programId) throws ApiException, DoesNotExistException {
+        Program program = programService.getById(programId).orElseThrow(() -> new DoesNotExistException("Program id does not exist"));
+        ObservationUnitsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), ObservationUnitsApi.class);
+        try {
+            if (!brAPIObservationUnitList.isEmpty()) {
+                Callable<Map<String, BrAPIObservationUnit>> postFunction = () -> {
+                    preprocessObservationUnits(brAPIObservationUnitList);
+                    List<BrAPIObservationUnit> ous = brAPIDAOUtil.post(brAPIObservationUnitList, api::observationunitsPost);
+                    return processObservationUnitsForCache(ous, program, false);
+                };
+                return programObservationUnitCache.post(programId, postFunction);
+            }
+            return new ArrayList<>();
+        } catch (Exception e) {
+            throw new InternalServerException("Unknown error has occurred: " + e.getMessage(), e);
+        }
+    }
+
     public List<BrAPIObservationUnit> getObservationUnitsById(Collection<String> observationUnitExternalIds, Program program) throws ApiException {
         if(observationUnitExternalIds.isEmpty()) {
             return Collections.emptyList();
@@ -231,6 +254,21 @@ public List<BrAPIObservationUnit> getObservationUnitsForDataset(@NotNull String
                 .collect(Collectors.toList());
     }
 
+    public List<BrAPIObservationUnit> getObservationUnitsForDatasetAndEnvs(@NotNull String datasetId, Collection<String> envIds, @NotNull Program program) throws ApiException {
+        String datasetReferenceSource = Utilities.generateReferenceSource(referenceSource, ExternalReferenceSource.DATASET);
+        String studyReferenceSource = Utilities.generateReferenceSource(referenceSource, ExternalReferenceSource.STUDIES);
+        return getProgramObservationUnits(program.getId()).values().stream()
+                .filter(ou -> {
+                    Optional<BrAPIExternalReference> datasetExRef = Utilities.getExternalReference(ou.getExternalReferences(), datasetReferenceSource);
+                    Optional<BrAPIExternalReference> studyExRef = Utilities.getExternalReference(ou.getExternalReferences(), studyReferenceSource);
+                    return Boolean.logicalAnd(
+                            datasetExRef.map(x -> x.getReferenceId().equals(datasetId)).orElse(false),
+                            studyExRef.map(x -> envIds.contains(x.getReferenceId())).orElse(false)
+                    );
+                })
+                .collect(Collectors.toList());
+    }
+
     // Note: does not use cache, impractical to implement all search parameters client-side.
     public List<BrAPIObservationUnit> getObservationUnits(Program program,
                                                           Optional<String> observationUnitId,
diff --git a/src/main/java/org/breedinginsight/brapi/v2/model/request/query/ExperimentExportQuery.java b/src/main/java/org/breedinginsight/brapi/v2/model/request/query/ExperimentExportQuery.java
index 8c59be52c..01782c319 100644
--- a/src/main/java/org/breedinginsight/brapi/v2/model/request/query/ExperimentExportQuery.java
+++ b/src/main/java/org/breedinginsight/brapi/v2/model/request/query/ExperimentExportQuery.java
@@ -12,7 +12,7 @@
 @ToString
 public class ExperimentExportQuery {
     private FileType fileExtension;
-    private String dataset;
+    private String datasetId;
     private String environments;
     @NotNull
     private boolean includeTimestamps;
diff --git a/src/main/java/org/breedinginsight/brapi/v2/services/BrAPIObservationVariableService.java b/src/main/java/org/breedinginsight/brapi/v2/services/BrAPIObservationVariableService.java
index f9742fb74..96a21cd14 100644
--- a/src/main/java/org/breedinginsight/brapi/v2/services/BrAPIObservationVariableService.java
+++ b/src/main/java/org/breedinginsight/brapi/v2/services/BrAPIObservationVariableService.java
@@ -31,6 +31,7 @@
 import org.breedinginsight.model.*;
 import org.breedinginsight.services.ProgramService;
 import org.breedinginsight.services.exceptions.DoesNotExistException;
+import org.breedinginsight.utilities.DatasetUtil;
 import org.breedinginsight.utilities.Utilities;
 import org.jetbrains.annotations.NotNull;
 
@@ -55,6 +56,8 @@ public BrAPIObservationVariableService(
         this.referenceSource = referenceSource;
     }
 
+    // TODO: support sub-entity datasets.
+    // This gets the observation variables for the top-level dataset in an experiment.
     public List<Trait> getBrAPIObservationVariablesForExperiment(
             UUID programId,
             Optional<String> experimentId,
@@ -78,12 +81,10 @@ public List<Trait> getBrAPIObservationVariablesForExperiment(
         }
 
         BrAPITrial experiment = trialService.getExperiment(program.get(), expId);
-        if(experiment
-                .getAdditionalInfo().getAsJsonObject()
-                .has(BrAPIAdditionalInfoFields.OBSERVATION_DATASET_ID)) {
-            String obsDatasetId = experiment
-                    .getAdditionalInfo().getAsJsonObject()
-                    .get(BrAPIAdditionalInfoFields.OBSERVATION_DATASET_ID).getAsString();
+        if(!experiment.getAdditionalInfo().getAsJsonArray(BrAPIAdditionalInfoFields.DATASETS).isEmpty()) {
+            String obsDatasetId = DatasetUtil
+                    .getTopLevelDatasetFromJson(experiment.getAdditionalInfo().getAsJsonArray(BrAPIAdditionalInfoFields.DATASETS))
+                    .getId().toString();
             return trialService.getDatasetObsVars(obsDatasetId, program.get());
         }
 
diff --git a/src/main/java/org/breedinginsight/brapi/v2/services/BrAPITrialService.java b/src/main/java/org/breedinginsight/brapi/v2/services/BrAPITrialService.java
index dd9bde018..192739ccb 100644
--- a/src/main/java/org/breedinginsight/brapi/v2/services/BrAPITrialService.java
+++ b/src/main/java/org/breedinginsight/brapi/v2/services/BrAPITrialService.java
@@ -1,5 +1,7 @@
 package org.breedinginsight.brapi.v2.services;
 
+import com.google.gson.JsonArray;
+import com.google.gson.JsonElement;
 import com.github.filosganga.geogson.model.Coordinates;
 import com.github.filosganga.geogson.model.positions.SinglePosition;
 import com.google.gson.JsonObject;
@@ -16,6 +18,7 @@
 import org.brapi.v2.model.germ.BrAPIGermplasm;
 
 import org.brapi.v2.model.pheno.*;
+import org.breedinginsight.api.model.v1.request.SubEntityDatasetRequest;
 import org.breedinginsight.brapi.v2.constants.BrAPIAdditionalInfoFields;
 import org.breedinginsight.brapi.v2.dao.*;
 import org.breedinginsight.brapi.v2.model.request.query.ExperimentExportQuery;
@@ -33,6 +36,7 @@
 import org.breedinginsight.services.TraitService;
 import org.breedinginsight.services.exceptions.DoesNotExistException;
 import org.breedinginsight.services.parsers.experiment.ExperimentFileColumns;
+import org.breedinginsight.utilities.DatasetUtil;
 import org.breedinginsight.utilities.IntOrderComparator;
 import org.breedinginsight.utilities.FileUtil;
 import org.breedinginsight.utilities.Utilities;
@@ -57,6 +61,7 @@ public class BrAPITrialService {
     private final String referenceSource;
     private final BrAPITrialDAO trialDAO;
     private final BrAPIObservationDAO observationDAO;
+    private final BrAPIObservationUnitDAO observationUnitDAO;
     private final BrAPIListDAO listDAO;
 
     private final TraitService traitService;
@@ -71,6 +76,7 @@ public class BrAPITrialService {
     public BrAPITrialService(@Property(name = "brapi.server.reference-source") String referenceSource,
                              BrAPITrialDAO trialDAO,
                              BrAPIObservationDAO observationDAO,
+                             BrAPIObservationUnitDAO observationUnitDAO,
                              BrAPIListDAO listDAO,
                              TraitService traitService,
                              BrAPIStudyDAO studyDAO,
@@ -82,6 +88,7 @@ public BrAPITrialService(@Property(name = "brapi.server.reference-source") Strin
         this.referenceSource = referenceSource;
         this.trialDAO = trialDAO;
         this.observationDAO = observationDAO;
+        this.observationUnitDAO = observationUnitDAO;
         this.listDAO = listDAO;
         this.traitService = traitService;
         this.studyDAO = studyDAO;
@@ -126,7 +133,6 @@ public DownloadFile exportObservations(
         String logHash = UUID.randomUUID().toString();
         log.debug(logHash + ": exporting experiment: "+experimentId+", params: " + params);
         DownloadFile downloadFile;
-        boolean isDataset = false;
         List<BrAPIObservation> dataset = new ArrayList<>();
         List<Trait> obsVars = new ArrayList<>();
         Map<String, Map<String, Object>> rowByOUId = new HashMap<>();
@@ -154,44 +160,32 @@ public DownloadFile exportObservations(
         }
         expStudies.forEach(study -> studyByDbId.putIfAbsent(study.getStudyDbId(), study));
 
-        // get the OUs for the requested environments
+        // Get the OUs for the requested environments.
         log.debug(logHash + ": fetching OUs for export");
         List<BrAPIObservationUnit> ous = new ArrayList<>();
         Map<String, BrAPIObservationUnit> ouByOUDbId = new HashMap<>();
         try {
-            for (BrAPIStudy study: expStudies) {
-                List<BrAPIObservationUnit> studyOUs = ouDAO.getObservationUnitsForStudyDbId(study.getStudyDbId(), program);
-                studyOUs.forEach(ou -> ouByOUDbId.put(ou.getObservationUnitDbId(), ou));
-                ous.addAll(studyOUs);
+            if (requestedEnvIds.isEmpty()) {
+                ous.addAll(ouDAO.getObservationUnitsForDataset(params.getDatasetId(), program));
+            } else {
+                ous.addAll(ouDAO.getObservationUnitsForDatasetAndEnvs(params.getDatasetId(), requestedEnvIds, program));
             }
+            ous.forEach(ou -> ouByOUDbId.put(ou.getObservationUnitDbId(), ou));
         } catch (ApiException err) {
             log.error(logHash + ": Error fetching observation units for a study by its DbId" +
                     Utilities.generateApiExceptionLogMessage(err), err);
         }
+        if (params.getDatasetId() != null) {
+            log.debug(logHash + ": fetching " + params.getDatasetId() + " dataset observation variables for export");
+            obsVars = getDatasetObsVars(params.getDatasetId(), program);
 
-        if ((StringUtils.isBlank(params.getDataset()) || "observations".equalsIgnoreCase(params.getDataset())) &&
-                experiment.getAdditionalInfo().getAsJsonObject().get(BrAPIAdditionalInfoFields.OBSERVATION_DATASET_ID) != null) {
-            String obsDatasetId = experiment
-                    .getAdditionalInfo().getAsJsonObject()
-                    .get(BrAPIAdditionalInfoFields.OBSERVATION_DATASET_ID).getAsString();
-            isDataset = true;
-            log.debug(logHash + ": fetching dataset observation variables for export");
-            obsVars = getDatasetObsVars(obsDatasetId, program);
-
-            // make additional columns in the export for each obs variable and obs variable timestamp
+            // Make additional columns in the export for each obs variable and obs variable timestamp.
             addObsVarColumns(columns, obsVars, params.isIncludeTimestamps(), program);
-
         }
 
-        // make export rows from any observations
-        if (isDataset) {
-            log.debug(logHash + ": fetching observations for export");
-            dataset = observationDAO.getObservationsByTrialDbId(List.of(experiment.getTrialDbId()), program);
-        }
-        if (!requestedEnvIds.isEmpty()) {
-            log.debug(logHash + ": filtering observations to only requested environments for export");
-            dataset = filterDatasetByEnvironment(dataset, requestedEnvIds, studyByDbId);
-        }
+        // Make export rows from any observations.
+        log.debug(logHash + ": fetching observations for export");
+        dataset = observationDAO.getObservationsByObservationUnits(ouByOUDbId.keySet(), program);
 
         log.debug(logHash + ": fetching program's germplasm for export");
         List<BrAPIGermplasm> programGermplasm = germplasmDAO.getGermplasmsByDBID(ouByOUDbId.values().stream().map(BrAPIObservationUnit::getGermplasmDbId).collect(Collectors.toList()), program.getId());
@@ -212,7 +206,6 @@ public DownloadFile exportObservations(
                 programGermplasmByDbId
         );
 
-
         // make export rows for OUs without observations
         if (rowByOUId.size() < ous.size()) {
             for (BrAPIObservationUnit ou: ous) {
@@ -247,7 +240,8 @@ public DownloadFile exportObservations(
                 List<Map<String, Object>> rows = entry.getValue();
                 sortDefaultForExportRows(rows);
                 StreamedFile streamedFile = FileUtil.writeToStreamedFile(columns, rows, fileType, SHEET_NAME);
-                String name = makeFileName(experiment, program, studyByDbId.get(entry.getKey()).getStudyName()) + fileType.getExtension();
+                // TODO: [BI-2183] remove hardcoded datasetName, use observation level.
+                String name = makeFileName(experiment, program, studyByDbId.get(entry.getKey()).getStudyName(), "Observation Dataset") + fileType.getExtension();
                 // Add to file list.
                 files.add(new DownloadFile(name, streamedFile));
             }
@@ -268,7 +262,8 @@ public DownloadFile exportObservations(
             StreamedFile streamedFile = FileUtil.writeToStreamedFile(columns, exportRows, fileType, SHEET_NAME);
             // Set filename.
             String envFilenameFragment = params.getEnvironments() == null ? "All Environments" : params.getEnvironments();
-            String fileName = makeFileName(experiment, program, envFilenameFragment) + fileType.getExtension();
+            // TODO: [BI-2183] remove hardcoded datasetName, use observation level.
+            String fileName = makeFileName(experiment, program, envFilenameFragment, "Observation Dataset") + fileType.getExtension();
             downloadFile = new DownloadFile(fileName, streamedFile);
         }
 
@@ -301,19 +296,19 @@ private StreamedFile zipFiles(List<DownloadFile> files) throws IOException {
         return new StreamedFile(in, new MediaType(MediaType.APPLICATION_OCTET_STREAM));
     }
 
-    public Dataset getDatasetData(Program program, UUID experimentId, UUID datsetId, Boolean stats) throws ApiException, DoesNotExistException {
-        log.debug("fetching dataset: " + datsetId + " for experiment: " + experimentId + ".  including stats: " + stats);
-        log.debug("fetching observationUnits for dataset: " + datsetId);
-        List<BrAPIObservationUnit> datasetOUs = ouDAO.getObservationUnitsForDataset(datsetId.toString(), program);
-        log.debug("fetching dataset variables dataset: " + datsetId);
-        List<Trait> datasetObsVars = getDatasetObsVars(datsetId.toString(), program);
+    public Dataset getDatasetData(Program program, UUID experimentId, UUID datasetId, Boolean stats) throws ApiException, DoesNotExistException {
+        log.debug("fetching dataset: " + datasetId + " for experiment: " + experimentId + ".  including stats: " + stats);
+        log.debug("fetching observationUnits for dataset: " + datasetId);
+        List<BrAPIObservationUnit> datasetOUs = ouDAO.getObservationUnitsForDataset(datasetId.toString(), program);
+        log.debug("fetching dataset variables dataset: " + datasetId);
+        List<Trait> datasetObsVars = getDatasetObsVars(datasetId.toString(), program);
         List<String> ouDbIds = datasetOUs.stream().map(BrAPIObservationUnit::getObservationUnitDbId).collect(Collectors.toList());
         List<String> obsVarDbIds = datasetObsVars.stream().map(Trait::getObservationVariableDbId).collect(Collectors.toList());
-        log.debug("fetching observations for dataset: " + datsetId);
+        log.debug("fetching observations for dataset: " + datasetId);
         List<BrAPIObservation> data = observationDAO.getObservationsByObservationUnitsAndVariables(ouDbIds, obsVarDbIds, program);
-        log.debug("building dataset object for dataset: " + datsetId);
+        log.debug("building dataset object for dataset: " + datasetId);
         sortDefaultForObservationUnit(datasetOUs);
-        Dataset dataset = new Dataset(experimentId.toString(), data, datasetOUs, datasetObsVars);
+        Dataset dataset = new Dataset(datasetId.toString(), experimentId.toString(), data, datasetOUs, datasetObsVars);
         if (stats) {
             Integer ouCount = datasetOUs.size();
             Integer obsVarCount = datasetObsVars.size();
@@ -330,6 +325,206 @@ public Dataset getDatasetData(Program program, UUID experimentId, UUID datsetId,
         return dataset;
     }
 
+    /**
+     * Retrieves the metadata of datasets associated with a program and experiment.
+     *
+     * @param program The program object representing the program that the datasets belong to.
+     * @param experimentId The UUID of the experiment that the datasets are associated with.
+     * @return A list of DatasetMetadata objects containing the metadata of the datasets.
+     * @throws DoesNotExistException If the trial does not exist for the program and experimentId combination.
+     * @throws ApiException If there is an error retrieving the trial or parsing the datasets metadata.
+     */
+    public List<DatasetMetadata> getDatasetsMetadata(Program program, UUID experimentId) throws DoesNotExistException, ApiException {
+        BrAPITrial trial = trialDAO.getTrialById(program.getId(), experimentId).orElseThrow(() -> new DoesNotExistException("Trial does not exist"));
+        JsonArray datasetsJson = trial.getAdditionalInfo().getAsJsonArray(BrAPIAdditionalInfoFields.DATASETS);
+        List<DatasetMetadata> datasets = DatasetUtil.datasetsFromJson(datasetsJson);
+        return datasets;
+    }
+
+    public Dataset createSubEntityDataset(Program program, UUID experimentId, SubEntityDatasetRequest request) throws ApiException, DoesNotExistException {
+        log.debug("creating sub-entity dataset: \"" + request.getName() + "\" for experiment: \"" + experimentId + "\" with: \"" + request.getRepeatedMeasures() + "\" repeated measures.");
+        UUID subEntityDatasetId = UUID.randomUUID();
+        List<BrAPIObservationUnit> subObsUnits = new ArrayList<>();
+        BrAPITrial experiment = getExperiment(program, experimentId);
+        // Get top level dataset ObservationUnits.
+        DatasetMetadata topLevelDataset = DatasetUtil.getTopLevelDataset(experiment);
+        if (topLevelDataset == null) {
+            log.error("Experiment {} has no top level dataset.", experiment.getTrialDbId());
+            throw new RuntimeException("Cannot create sub-entity dataset for experiment without top level dataset.");
+        }
+
+        List<BrAPIObservationUnit> expOUs = ouDAO.getObservationUnitsForDataset(topLevelDataset.getId().toString(), program);
+        for (BrAPIObservationUnit expUnit : expOUs) {
+
+            // Get environment number from study.
+            String envSeqValue = studyDAO.getStudyByDbId(expUnit.getStudyDbId(), program).orElseThrow()
+                    .getAdditionalInfo().get(BrAPIAdditionalInfoFields.ENVIRONMENT_NUMBER).getAsString();
+
+            for (int i=1; i<=request.getRepeatedMeasures(); i++) {
+                // Create subObsUnit and add to list.
+                subObsUnits.add(
+                    createSubObservationUnit(
+                        request.getName(),
+                        Integer.toString(i),
+                        program,
+                        envSeqValue,
+                        expUnit,
+                        this.referenceSource,
+                        subEntityDatasetId,
+                        UUID.randomUUID()
+                    )
+                );
+            }
+        }
+
+        List<BrAPIObservationUnit> createdObservationUnits = observationUnitDAO.createBrAPIObservationUnits(subObsUnits, program.getId());
+
+        // Add the new dataset metadata to the datasets array in the trial's additionalInfo.
+        DatasetMetadata subEntityDatasetMetadata = DatasetMetadata.builder()
+                .id(subEntityDatasetId)
+                .name(request.getName())
+                .level(DatasetLevel.SUB_OBS_UNIT)
+                .build();
+        List<DatasetMetadata> datasets = DatasetUtil.datasetsFromJson(experiment.getAdditionalInfo().getAsJsonArray(BrAPIAdditionalInfoFields.DATASETS));
+        datasets.add(subEntityDatasetMetadata);
+        experiment.getAdditionalInfo().add(BrAPIAdditionalInfoFields.DATASETS, DatasetUtil.jsonArrayFromDatasets(datasets));
+        // Ask the DAO to persist the updated trial.
+        trialDAO.updateBrAPITrial(experiment.getTrialDbId(), experiment, program.getId());
+
+        // Return the new dataset.
+        return getDatasetData(program, experimentId, subEntityDatasetId, false);
+    }
+
+    public BrAPIObservationUnit createSubObservationUnit(
+            String subEntityDatasetName,
+            String subUnitId,
+            Program program,
+            String seqVal,
+            BrAPIObservationUnit expUnit,
+            String referenceSource,
+            UUID datasetId,
+            UUID id
+    ) {
+
+        BrAPIObservationUnit observationUnit = new BrAPIObservationUnit();
+        observationUnit.setObservationUnitName(Utilities.appendProgramKey(subUnitId, program.getKey(), seqVal));
+
+        // Build ExternalReferences.
+        List<BrAPIExternalReference> refs = new ArrayList<>();
+
+        // Program ref.
+        Utilities.addReference(refs, program.getId(), referenceSource, ExternalReferenceSource.PROGRAMS);
+
+        // Trial and Study refs can be copied from expUnit to subUnit.
+        Utilities.getExternalReference(expUnit.getExternalReferences(), referenceSource, ExternalReferenceSource.TRIALS)
+            .ifPresent(refs::add);
+        Utilities.getExternalReference(expUnit.getExternalReferences(), referenceSource, ExternalReferenceSource.STUDIES)
+            .ifPresent(refs::add);
+
+        // Dataset and ObservationUnit refs are specific to the subUnit.
+        if (datasetId != null) {
+            Utilities.addReference(refs, datasetId, referenceSource, ExternalReferenceSource.DATASET);
+        }
+        if (id != null) {
+            Utilities.addReference(refs, id, referenceSource, ExternalReferenceSource.OBSERVATION_UNITS);
+        }
+
+        // Set ExternalReferences.
+        observationUnit.setExternalReferences(refs);
+
+        // Set Trial.
+        observationUnit.setTrialName(expUnit.getTrialName());
+        observationUnit.setTrialDbId(expUnit.getTrialDbId());
+
+        // Set Study.
+        observationUnit.setStudyName(expUnit.getStudyName());
+        observationUnit.setStudyDbId(expUnit.getStudyDbId());
+
+        // Set Germplasm.
+        observationUnit.setGermplasmName(expUnit.getGermplasmName());
+        observationUnit.setGermplasmDbId(expUnit.getGermplasmDbId());
+        JsonElement gid = expUnit.getAdditionalInfo().get(BrAPIAdditionalInfoFields.GID);
+        if (gid != null) {
+            observationUnit.putAdditionalInfoItem(BrAPIAdditionalInfoFields.GID, gid.getAsString());
+        }
+
+        // Set treatment factors.
+        List<BrAPIObservationTreatment> treatmentFactors = new ArrayList<>();
+        for (BrAPIObservationTreatment t : expUnit.getTreatments()) {
+            BrAPIObservationTreatment treatment = new BrAPIObservationTreatment();
+            treatment.setFactor(t.getFactor());
+            treatment.setModality(t.getModality());
+            treatmentFactors.add(treatment);
+        }
+        observationUnit.setTreatments(treatmentFactors);
+
+        // Put level in additional info: keep this in case we decide to rename levels in future.
+        observationUnit.putAdditionalInfoItem(BrAPIAdditionalInfoFields.OBSERVATION_LEVEL, subEntityDatasetName);
+        // Put RTK in additional info.
+        JsonElement rtk = expUnit.getAdditionalInfo().get(BrAPIAdditionalInfoFields.RTK);
+        if (rtk != null) {
+            observationUnit.putAdditionalInfoItem(BrAPIAdditionalInfoFields.RTK, rtk.getAsString());
+        }
+
+        // Build ObservationUnitPosition.
+        BrAPIObservationUnitPosition position = new BrAPIObservationUnitPosition();
+
+        // Set subUnit's basic position attributes from expUnit.
+        position.setEntryType(expUnit.getObservationUnitPosition().getEntryType());
+        position.setGeoCoordinates(expUnit.getObservationUnitPosition().getGeoCoordinates());
+        position.setPositionCoordinateX(expUnit.getObservationUnitPosition().getPositionCoordinateX());
+        position.setPositionCoordinateY(expUnit.getObservationUnitPosition().getPositionCoordinateY());
+        position.setPositionCoordinateXType(expUnit.getObservationUnitPosition().getPositionCoordinateXType());
+        position.setPositionCoordinateYType(expUnit.getObservationUnitPosition().getPositionCoordinateYType());
+
+        // ObservationLevel entry for Sub-Obs Unit.
+        BrAPIObservationUnitLevelRelationship level = new BrAPIObservationUnitLevelRelationship();
+        // TODO: consider removing toLowerCase() after BI-2219 is implemented.
+        level.setLevelName(subEntityDatasetName.toLowerCase());
+        level.setLevelCode(Utilities.appendProgramKey(subUnitId, program.getKey(), seqVal));
+        level.setLevelOrder(DatasetLevel.SUB_OBS_UNIT.getValue());
+        position.setObservationLevel(level);
+
+        // ObservationLevelRelationships.
+        List<BrAPIObservationUnitLevelRelationship> levelRelationships = new ArrayList<>();
+        // ObservationLevelRelationships for block.
+        BrAPIObservationUnitLevelRelationship expBlockLevel = expUnit.getObservationUnitPosition()
+                .getObservationLevelRelationships().stream()
+                .filter(x -> x.getLevelName().equals(BrAPIConstants.REPLICATE.getValue())).findFirst().orElse(null);
+        if (expBlockLevel != null) {
+            BrAPIObservationUnitLevelRelationship blockLevel = new BrAPIObservationUnitLevelRelationship();
+            blockLevel.setLevelName(expBlockLevel.getLevelName());
+            blockLevel.setLevelCode(expBlockLevel.getLevelCode());
+            blockLevel.setLevelOrder(expBlockLevel.getLevelOrder());
+            levelRelationships.add(blockLevel);
+        }
+        // ObservationLevelRelationships for rep.
+        BrAPIObservationUnitLevelRelationship expRepLevel = expUnit.getObservationUnitPosition()
+                .getObservationLevelRelationships().stream()
+                .filter(x -> x.getLevelName().equals(BrAPIConstants.BLOCK.getValue())).findFirst().orElse(null);
+        if (expRepLevel != null) {
+            BrAPIObservationUnitLevelRelationship repLevel = new BrAPIObservationUnitLevelRelationship();
+            repLevel.setLevelName(expRepLevel.getLevelName());
+            repLevel.setLevelCode(expRepLevel.getLevelCode());
+            repLevel.setLevelOrder(expRepLevel.getLevelOrder());
+            levelRelationships.add(repLevel);
+        }
+        // ObservationLevelRelationships for top-level Exp Unit linking.
+        BrAPIObservationUnitLevelRelationship expUnitLevel = new BrAPIObservationUnitLevelRelationship();
+        // TODO: consider removing toLowerCase() after BI-2219 is implemented.
+        expUnitLevel.setLevelName(expUnit.getAdditionalInfo().get(BrAPIAdditionalInfoFields.OBSERVATION_LEVEL).getAsString().toLowerCase());
+        String expUnitUUID = Utilities.getExternalReference(expUnit.getExternalReferences(), referenceSource, ExternalReferenceSource.OBSERVATION_UNITS).orElseThrow().getReferenceId();
+        expUnitLevel.setLevelCode(Utilities.appendProgramKey(expUnitUUID, program.getKey(), seqVal));
+        expUnitLevel.setLevelOrder(DatasetLevel.EXP_UNIT.getValue());
+        levelRelationships.add(expUnitLevel);
+        position.setObservationLevelRelationships(levelRelationships);
+
+        // Set ObservationUnitPosition.
+        observationUnit.setObservationUnitPosition(position);
+
+        return observationUnit;
+    }
+
     private void addBrAPIObsToRecords(
             List<BrAPIObservation> dataset,
             BrAPITrial experiment,
@@ -564,12 +759,14 @@ private void addObsVarColumns(
             }
         }
     }
-    private String makeFileName(BrAPITrial experiment, Program program, String envName) {
-        // <exp-title>_Observation Dataset_<environment>_<export-timestamp>
+
+    private String makeFileName(BrAPITrial experiment, Program program, String envName, String datasetName) {
+        // <exp-title>_<dataset-name>_<environment>_<export-timestamp>
         DateTimeFormatter formatter = DateTimeFormatter.ofPattern("yyyy-MM-dd_hh-mm-ssZ");
         String timestamp = formatter.format(OffsetDateTime.now());
-        String unsafeName = String.format("%s_Observation Dataset_%s_%s",
+        String unsafeName = String.format("%s_%s_%s_%s",
                 Utilities.removeProgramKey(experiment.getTrialName(), program.getKey()),
+                datasetName,
                 Utilities.removeProgramKeyAndUnknownAdditionalData(envName, program.getKey()),
                 timestamp);
         // Make file name safe for all platforms.
diff --git a/src/main/java/org/breedinginsight/brapps/importer/model/imports/experimentObservation/ExperimentObservation.java b/src/main/java/org/breedinginsight/brapps/importer/model/imports/experimentObservation/ExperimentObservation.java
index 579c34a31..0f2596e6f 100644
--- a/src/main/java/org/breedinginsight/brapps/importer/model/imports/experimentObservation/ExperimentObservation.java
+++ b/src/main/java/org/breedinginsight/brapps/importer/model/imports/experimentObservation/ExperimentObservation.java
@@ -33,10 +33,7 @@
 import org.breedinginsight.brapps.importer.model.config.*;
 import org.breedinginsight.brapps.importer.model.imports.BrAPIImport;
 import org.breedinginsight.brapps.importer.services.ExternalReferenceSource;
-import org.breedinginsight.model.BrAPIConstants;
-import org.breedinginsight.model.Program;
-import org.breedinginsight.model.ProgramLocation;
-import org.breedinginsight.model.User;
+import org.breedinginsight.model.*;
 import org.breedinginsight.utilities.Utilities;
 
 import java.math.BigInteger;
@@ -246,9 +243,9 @@ public BrAPIListDetails constructDatasetDetails(
         dataSetDetails.setData(new ArrayList<>());
         dataSetDetails.putAdditionalInfoItem("datasetType", "observationDataset");
         List<BrAPIExternalReference> refs = new ArrayList<>();
-        addReference(refs, program.getId(), referenceSourceBase, ExternalReferenceSource.PROGRAMS);
-        addReference(refs, UUID.fromString(trialId), referenceSourceBase, ExternalReferenceSource.TRIALS);
-        addReference(refs, datasetId, referenceSourceBase, ExternalReferenceSource.DATASET);
+        Utilities.addReference(refs, program.getId(), referenceSourceBase, ExternalReferenceSource.PROGRAMS);
+        Utilities.addReference(refs, UUID.fromString(trialId), referenceSourceBase, ExternalReferenceSource.TRIALS);
+        Utilities.addReference(refs, datasetId, referenceSourceBase, ExternalReferenceSource.DATASET);
         dataSetDetails.setExternalReferences(refs);
         return dataSetDetails;
     }
@@ -284,7 +281,12 @@ public BrAPIObservationUnit constructBrAPIObservationUnit(
 
         BrAPIObservationUnitPosition position = new BrAPIObservationUnitPosition();
         BrAPIObservationUnitLevelRelationship level = new BrAPIObservationUnitLevelRelationship();
-        level.setLevelName("plot");  //BreedBase only accepts "plot" or "plant"
+        // If expUnit is null, a validation error will be produced later on.
+        if (getExpUnit() != null)
+        {
+            // TODO: [BI-2219] BJTS only accepts hardcoded levels, need to handle dynamic levels.
+            level.setLevelName(getExpUnit().toLowerCase());  // HACK: toLowerCase() is needed to match BJTS hardcoded levels.
+        }
         level.setLevelCode(Utilities.appendProgramKey(getExpUnitId(), program.getKey(), seqVal));
         position.setObservationLevel(level);
         observationUnit.putAdditionalInfoItem(BrAPIAdditionalInfoFields.OBSERVATION_LEVEL, getExpUnit());
@@ -413,21 +415,21 @@ private List<BrAPIExternalReference> getBrAPIExternalReferences(
             Program program, String referenceSourceBaseName, UUID trialId, UUID datasetId, UUID studyId, UUID obsUnitId, UUID observationId) {
         List<BrAPIExternalReference> refs = new ArrayList<>();
 
-        addReference(refs, program.getId(), referenceSourceBaseName, ExternalReferenceSource.PROGRAMS);
+        Utilities.addReference(refs, program.getId(), referenceSourceBaseName, ExternalReferenceSource.PROGRAMS);
         if (trialId != null) {
-            addReference(refs, trialId, referenceSourceBaseName, ExternalReferenceSource.TRIALS);
+            Utilities.addReference(refs, trialId, referenceSourceBaseName, ExternalReferenceSource.TRIALS);
         }
         if (datasetId != null) {
-            addReference(refs, datasetId, referenceSourceBaseName, ExternalReferenceSource.DATASET);
+            Utilities.addReference(refs, datasetId, referenceSourceBaseName, ExternalReferenceSource.DATASET);
         }
         if (studyId != null) {
-            addReference(refs, studyId, referenceSourceBaseName, ExternalReferenceSource.STUDIES);
+            Utilities.addReference(refs, studyId, referenceSourceBaseName, ExternalReferenceSource.STUDIES);
         }
         if (obsUnitId != null) {
-            addReference(refs, obsUnitId, referenceSourceBaseName, ExternalReferenceSource.OBSERVATION_UNITS);
+            Utilities.addReference(refs, obsUnitId, referenceSourceBaseName, ExternalReferenceSource.OBSERVATION_UNITS);
         }
         if (observationId != null) {
-            addReference(refs, observationId, referenceSourceBaseName, ExternalReferenceSource.OBSERVATIONS);
+            Utilities.addReference(refs, observationId, referenceSourceBaseName, ExternalReferenceSource.OBSERVATIONS);
         }
 
         return refs;
@@ -453,14 +455,6 @@ private List<BrAPIExternalReference> getObservationExternalReferences(
         return getBrAPIExternalReferences(program, referenceSourceBaseName, trialId, null, studyId, obsUnitId, observationId);
     }
 
-
-    private void addReference(List<BrAPIExternalReference> refs, UUID uuid, String referenceBaseNameSource, ExternalReferenceSource refSourceName) {
-        BrAPIExternalReference reference = new BrAPIExternalReference();
-        reference.setReferenceSource(String.format("%s/%s", referenceBaseNameSource, refSourceName.getName()));
-        reference.setReferenceID(uuid.toString());
-        refs.add(reference);
-    }
-
     public static final class Columns {
         public static final String GERMPLASM_NAME = "Germplasm Name";
         public static final String GERMPLASM_GID = "Germplasm GID";
diff --git a/src/main/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java b/src/main/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java
index 95e196c5b..c0f5c4c1f 100644
--- a/src/main/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java
+++ b/src/main/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java
@@ -65,6 +65,7 @@
 import org.breedinginsight.services.exceptions.MissingRequiredInfoException;
 import org.breedinginsight.services.exceptions.UnprocessableEntityException;
 import org.breedinginsight.services.exceptions.ValidatorException;
+import org.breedinginsight.utilities.DatasetUtil;
 import org.breedinginsight.utilities.Utilities;
 import org.jooq.DSLContext;
 import tech.tablesaw.api.Table;
@@ -1159,9 +1160,11 @@ private PendingImportObject<BrAPIObservationUnit> fetchOrCreateObsUnitPIO(Progra
             UUID trialID = trialPIO.getId();
             UUID datasetId = null;
             if (commit) {
-                datasetId = UUID.fromString(trialPIO.getBrAPIObject()
-                        .getAdditionalInfo().getAsJsonObject()
-                        .get(BrAPIAdditionalInfoFields.OBSERVATION_DATASET_ID).getAsString());
+                JsonArray datasetsJson = trialPIO.getBrAPIObject().getAdditionalInfo().getAsJsonArray(BrAPIAdditionalInfoFields.DATASETS);
+                DatasetMetadata dataset = DatasetUtil.getDatasetByNameFromJson(datasetsJson, importRow.getExpUnit());
+                 if (dataset != null) {
+                     datasetId = dataset.getId();
+                 }
             }
             PendingImportObject<BrAPIStudy> studyPIO = this.studyByNameNoScope.get(importRow.getEnv());
             UUID studyID = studyPIO.getId();
@@ -1302,6 +1305,7 @@ private void addObsVarsToDatasetDetails(PendingImportObject<BrAPIListDetails> pi
             }
         });
     }
+
     private void fetchOrCreateDatasetPIO(ExperimentObservation importRow, Program program, List<Trait> referencedTraits) throws UnprocessableEntityException {
         PendingImportObject<BrAPIListDetails> pio;
         PendingImportObject<BrAPITrial> trialPIO = hasAllReferenceUnitIds ?
@@ -1323,7 +1327,22 @@ private void fetchOrCreateDatasetPIO(ExperimentObservation importRow, Program pr
                     program,
                     trialPIO.getId().toString());
             pio = new PendingImportObject<BrAPIListDetails>(ImportObjectState.NEW, newDataset, id);
-            trialPIO.getBrAPIObject().putAdditionalInfoItem("observationDatasetId", id.toString());
+
+            JsonArray datasetsJson = trialPIO.getBrAPIObject().getAdditionalInfo().getAsJsonArray(BrAPIAdditionalInfoFields.DATASETS);
+            // If datasets property does not yet exist, create it
+            String datasetName = StringUtils.isNotBlank(importRow.getSubObsUnit()) ? importRow.getSubObsUnit() : importRow.getExpUnit();
+            List<DatasetMetadata> datasets = DatasetUtil.datasetsFromJson(datasetsJson);
+            DatasetMetadata dataset = DatasetMetadata.builder()
+                    .name(datasetName)
+                    .id(id)
+                    .level(StringUtils.isNotBlank(importRow.getSubObsUnit()) ? DatasetLevel.SUB_OBS_UNIT : DatasetLevel.EXP_UNIT)
+                    .build();
+
+            log.debug(dataset.getName());
+            datasets.add(dataset);
+            datasetsJson = DatasetUtil.jsonArrayFromDatasets(datasets);
+            trialPIO.getBrAPIObject().getAdditionalInfo().add(BrAPIAdditionalInfoFields.DATASETS, datasetsJson);
+
             if (ImportObjectState.EXISTING == trialPIO.getState()) {
                 trialPIO.setState(ImportObjectState.MUTATED);
             }
@@ -2035,8 +2054,9 @@ private Map<String, PendingImportObject<BrAPIListDetails>> mapPendingObsDatasetB
             Map<String, PendingImportObject<BrAPITrial>> trialByOUId,
             Map<String, PendingImportObject<BrAPIListDetails>> obsVarDatasetByName,
             Map<String, PendingImportObject<BrAPIListDetails>> obsVarDatasetByOUId) {
-        if (!trialByOUId.isEmpty() && !obsVarDatasetByName.isEmpty() &&
-                trialByOUId.values().iterator().next().getBrAPIObject().getAdditionalInfo().has(BrAPIAdditionalInfoFields.OBSERVATION_DATASET_ID)) {
+        if (!trialByOUId.isEmpty() &&
+                !obsVarDatasetByName.isEmpty() &&
+                !trialByOUId.values().iterator().next().getBrAPIObject().getAdditionalInfo().getAsJsonArray(BrAPIAdditionalInfoFields.DATASETS).isEmpty()) {
             obsVarDatasetByOUId.put(unitId, obsVarDatasetByName.values().iterator().next());
         }
 
@@ -2051,17 +2071,18 @@ private Map<String, PendingImportObject<BrAPIListDetails>> mapPendingObsDatasetB
      * @return A map of observation variable dataset objects indexed by dataset name.
      * @throws InternalServerException If the existing dataset summary is not retrieved from the BrAPI server, or an error occurs during API communication.
      */
+    // TODO: add dataset name or id parameter? This only supports top level for now.
     private Map<String, PendingImportObject<BrAPIListDetails>> initializeObsVarDatasetForExistingObservationUnits(
             Map<String, PendingImportObject<BrAPITrial>> trialByName,
             Program program) {
         Map<String, PendingImportObject<BrAPIListDetails>> obsVarDatasetByName = new HashMap<>();
 
         if (trialByName.size() > 0 &&
-                trialByName.values().iterator().next().getBrAPIObject().getAdditionalInfo().has(BrAPIAdditionalInfoFields.OBSERVATION_DATASET_ID)) {
-            String datasetId = trialByName.values().iterator().next().getBrAPIObject()
-                    .getAdditionalInfo()
-                    .get(BrAPIAdditionalInfoFields.OBSERVATION_DATASET_ID)
-                    .getAsString();
+                !trialByName.values().iterator().next().getBrAPIObject().getAdditionalInfo().getAsJsonArray(BrAPIAdditionalInfoFields.DATASETS).isEmpty()) {
+            String datasetId = DatasetUtil.getDatasetIdByNameFromJson(
+                    trialByName.values().iterator().next().getBrAPIObject().getAdditionalInfo().getAsJsonArray(BrAPIAdditionalInfoFields.DATASETS),
+                    trialByName.values().iterator().next().getBrAPIObject().getAdditionalInfo().get(BrAPIAdditionalInfoFields.DEFAULT_OBSERVATION_LEVEL).getAsString()
+                );
 
             try {
                 List<BrAPIListSummary> existingDatasets = brAPIListDAO
@@ -2089,11 +2110,10 @@ private Map<String, PendingImportObject<BrAPIListDetails>> initializeObsVarDatas
 
         Optional<PendingImportObject<BrAPITrial>> trialPIO = getTrialPIO(experimentImportRows);
 
-        if (trialPIO.isPresent() && trialPIO.get().getBrAPIObject().getAdditionalInfo().has(BrAPIAdditionalInfoFields.OBSERVATION_DATASET_ID)) {
-            String datasetId = trialPIO.get().getBrAPIObject()
-                    .getAdditionalInfo()
-                    .get(BrAPIAdditionalInfoFields.OBSERVATION_DATASET_ID)
-                    .getAsString();
+        if (trialPIO.isPresent() && !trialPIO.get().getBrAPIObject().getAdditionalInfo().getAsJsonArray(BrAPIAdditionalInfoFields.DATASETS).isEmpty()) {
+            String datasetId = DatasetUtil.getTopLevelDatasetFromJson(
+                        trialPIO.get().getBrAPIObject().getAdditionalInfo().getAsJsonArray(BrAPIAdditionalInfoFields.DATASETS)
+                    ).getId().toString();
           try {
             List<BrAPIListSummary> existingDatasets = brAPIListDAO
                     .getListByTypeAndExternalRef(BrAPIListTypes.OBSERVATIONVARIABLES,
diff --git a/src/main/java/org/breedinginsight/model/Dataset.java b/src/main/java/org/breedinginsight/model/Dataset.java
index 638c946f1..9cee40591 100644
--- a/src/main/java/org/breedinginsight/model/Dataset.java
+++ b/src/main/java/org/breedinginsight/model/Dataset.java
@@ -1,3 +1,22 @@
+
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
 package org.breedinginsight.model;
 
 import com.fasterxml.jackson.annotation.JsonInclude;
@@ -10,6 +29,7 @@
 
 @JsonInclude(JsonInclude.Include.NON_ABSENT)
 public class Dataset {
+    public String id;
     public String experimentId;
     public JsonObject additionalInfo;
     public List<BrAPIObservation> data;
@@ -31,10 +51,12 @@ public enum DatasetStat {
     }
 
     public Dataset(
+            String id,
             String experimentId,
             List<BrAPIObservation> data,
             List<BrAPIObservationUnit> observationUnits,
             List<Trait> observationVariables) {
+        this.id = id;
         this.experimentId = experimentId;
         this.additionalInfo = new JsonObject();
         this.data = data;
diff --git a/src/main/java/org/breedinginsight/model/DatasetLevel.java b/src/main/java/org/breedinginsight/model/DatasetLevel.java
new file mode 100644
index 000000000..8bad5078f
--- /dev/null
+++ b/src/main/java/org/breedinginsight/model/DatasetLevel.java
@@ -0,0 +1,42 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.breedinginsight.model;
+
+import com.fasterxml.jackson.annotation.JsonValue;
+import com.google.gson.annotations.SerializedName;
+
+// The @SerializedName annotations are to make gson serialize correctly in the data access layer.
+// The @JsonValue annotation is to make micronaut (via jackson) serialize correctly in the controller response.
+public enum DatasetLevel {
+    @SerializedName("0")
+    EXP_UNIT(0),
+    @SerializedName("1")
+    SUB_OBS_UNIT(1);
+
+    private final int value;
+
+    DatasetLevel(int value) {
+        this.value = value;
+    }
+
+    @JsonValue
+    public int getValue() {
+        return value;
+    }
+
+}
\ No newline at end of file
diff --git a/src/main/java/org/breedinginsight/model/DatasetMetadata.java b/src/main/java/org/breedinginsight/model/DatasetMetadata.java
new file mode 100644
index 000000000..ca96c6256
--- /dev/null
+++ b/src/main/java/org/breedinginsight/model/DatasetMetadata.java
@@ -0,0 +1,38 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.breedinginsight.model;
+
+import lombok.Getter;
+import lombok.NoArgsConstructor;
+import lombok.Setter;
+import lombok.ToString;
+import lombok.experimental.Accessors;
+import lombok.experimental.SuperBuilder;
+import java.util.UUID;
+
+@Getter
+@Setter
+@Accessors(chain=true)
+@ToString
+@SuperBuilder
+@NoArgsConstructor
+public class DatasetMetadata {
+    private String name;
+    private UUID id;
+    private DatasetLevel level;
+}
\ No newline at end of file
diff --git a/src/main/java/org/breedinginsight/utilities/DatasetUtil.java b/src/main/java/org/breedinginsight/utilities/DatasetUtil.java
new file mode 100644
index 000000000..f64bbadc5
--- /dev/null
+++ b/src/main/java/org/breedinginsight/utilities/DatasetUtil.java
@@ -0,0 +1,65 @@
+package org.breedinginsight.utilities;
+
+import com.google.gson.Gson;
+import com.google.gson.JsonArray;
+import com.google.gson.reflect.TypeToken;
+import org.brapi.client.v2.JSON;
+import org.brapi.v2.model.core.BrAPITrial;
+import org.breedinginsight.brapi.v2.constants.BrAPIAdditionalInfoFields;
+import org.breedinginsight.model.DatasetLevel;
+import org.breedinginsight.model.DatasetMetadata;
+
+import java.lang.reflect.Type;
+import java.util.ArrayList;
+import java.util.List;
+
+public class DatasetUtil {
+
+    public static Type listDatasetType = new TypeToken<List<DatasetMetadata>>() {}.getType();
+    public static Gson gson = new JSON().getGson();
+
+    public static List<DatasetMetadata> datasetsFromJson(JsonArray datasetsJsonArray) {
+        if (datasetsJsonArray != null) {
+            return gson.fromJson(datasetsJsonArray, listDatasetType);
+        }
+
+        return new ArrayList<>();
+    }
+
+    public static JsonArray jsonArrayFromDatasets(List<DatasetMetadata> datasets) {
+        return gson.toJsonTree(datasets, listDatasetType).getAsJsonArray();
+    }
+
+    public static String getDatasetIdByNameFromJson(JsonArray datasetsJsonArray, String datasetName) {
+        DatasetMetadata dataset = getDatasetByNameFromJson(datasetsJsonArray, datasetName);
+        if (dataset != null) {
+            return dataset.getId().toString();
+        }
+        return null;
+    }
+
+    public static DatasetMetadata getDatasetByNameFromJson(JsonArray datasetsJsonArray, String datasetName) {
+        // Short-circuiting null check.
+        if (datasetsJsonArray == null || datasetName == null) {
+            return null;
+        }
+        List<DatasetMetadata> datasets = datasetsFromJson(datasetsJsonArray);
+        for (DatasetMetadata dataset : datasets) {
+            if (dataset.getName().equals(datasetName)) {
+                return dataset;
+            }
+        }
+        return null;
+    }
+
+    public static DatasetMetadata getTopLevelDatasetFromJson(JsonArray datasetsJsonArray) {
+        List<DatasetMetadata> datasets = datasetsFromJson(datasetsJsonArray);
+        // Return the top level dataset if it exists, otherwise null.
+        return datasets.stream().filter(dataset -> dataset.getLevel().equals(DatasetLevel.EXP_UNIT)).findFirst().orElse(null);
+    }
+
+    public static DatasetMetadata getTopLevelDataset(BrAPITrial experiment) {
+        return getTopLevelDatasetFromJson(experiment.getAdditionalInfo().getAsJsonArray(BrAPIAdditionalInfoFields.DATASETS));
+    }
+
+}
diff --git a/src/main/java/org/breedinginsight/utilities/Utilities.java b/src/main/java/org/breedinginsight/utilities/Utilities.java
index 2231f3a16..3d9d6d04c 100644
--- a/src/main/java/org/breedinginsight/utilities/Utilities.java
+++ b/src/main/java/org/breedinginsight/utilities/Utilities.java
@@ -191,6 +191,17 @@ public static Optional<BrAPIExternalReference> getExternalReference(List<BrAPIEx
         return externalReferences.stream().filter(externalReference -> externalReference.getReferenceSource().equals(source)).findFirst();
     }
 
+    public static Optional<BrAPIExternalReference> getExternalReference(List<BrAPIExternalReference> externalReferences, String referenceSourceBase, ExternalReferenceSource referenceSource) {
+        return getExternalReference(externalReferences, generateReferenceSource(referenceSourceBase, referenceSource));
+    }
+
+    public static void addReference(List<BrAPIExternalReference> refs, UUID uuid, String referenceBaseNameSource, ExternalReferenceSource refSourceName) {
+        BrAPIExternalReference reference = new BrAPIExternalReference();
+        reference.setReferenceSource(String.format("%s/%s", referenceBaseNameSource, refSourceName.getName()));
+        reference.setReferenceId(uuid.toString());
+        refs.add(reference);
+    }
+
     /**
      * For a list of items, if the list has only one item, return that item, otherwise return an empty {@link Optional}
      * @param items {@link List} of items
diff --git a/src/test/java/org/breedinginsight/brapi/v2/BrAPIObservationLevelsControllerIntegrationTest.java b/src/test/java/org/breedinginsight/brapi/v2/BrAPIObservationLevelsControllerIntegrationTest.java
index 85f6c6773..e38ab05fc 100644
--- a/src/test/java/org/breedinginsight/brapi/v2/BrAPIObservationLevelsControllerIntegrationTest.java
+++ b/src/test/java/org/breedinginsight/brapi/v2/BrAPIObservationLevelsControllerIntegrationTest.java
@@ -249,7 +249,7 @@ private String getEnvId(JsonObject result, int index) {
                 .get("brAPIObject").getAsJsonObject()
                 .get("externalReferences").getAsJsonArray()
                 .get(2).getAsJsonObject()
-                .get("referenceID").getAsString();
+                .get("referenceId").getAsString();
     }
 
     private List<BrAPIGermplasm> createGermplasm(int numToCreate) {
diff --git a/src/test/java/org/breedinginsight/brapi/v2/BrAPIObservationUnitControllerIntegrationTest.java b/src/test/java/org/breedinginsight/brapi/v2/BrAPIObservationUnitControllerIntegrationTest.java
index 3a3d8ffa3..bdfe304c0 100644
--- a/src/test/java/org/breedinginsight/brapi/v2/BrAPIObservationUnitControllerIntegrationTest.java
+++ b/src/test/java/org/breedinginsight/brapi/v2/BrAPIObservationUnitControllerIntegrationTest.java
@@ -381,7 +381,7 @@ private String getEnvId(JsonObject result, int index) {
                 .get("brAPIObject").getAsJsonObject()
                 .get("externalReferences").getAsJsonArray()
                 .get(2).getAsJsonObject()
-                .get("referenceID").getAsString();
+                .get("referenceId").getAsString();
     }
 
     private List<BrAPIGermplasm> createGermplasm(int numToCreate) {
diff --git a/src/test/java/org/breedinginsight/brapi/v2/BrAPIObservationsControllerIntegrationTest.java b/src/test/java/org/breedinginsight/brapi/v2/BrAPIObservationsControllerIntegrationTest.java
index 16d7261fb..5b4e562a6 100644
--- a/src/test/java/org/breedinginsight/brapi/v2/BrAPIObservationsControllerIntegrationTest.java
+++ b/src/test/java/org/breedinginsight/brapi/v2/BrAPIObservationsControllerIntegrationTest.java
@@ -337,7 +337,7 @@ private String getEnvId(JsonObject result, int index) {
                 .get("brAPIObject").getAsJsonObject()
                 .get("externalReferences").getAsJsonArray()
                 .get(2).getAsJsonObject()
-                .get("referenceID").getAsString();
+                .get("referenceId").getAsString();
     }
 
     private List<BrAPIGermplasm> createGermplasm(int numToCreate) {
diff --git a/src/test/java/org/breedinginsight/brapi/v2/BrAPIStudiesControllerIntegrationTest.java b/src/test/java/org/breedinginsight/brapi/v2/BrAPIStudiesControllerIntegrationTest.java
index ac276003c..faee28da4 100644
--- a/src/test/java/org/breedinginsight/brapi/v2/BrAPIStudiesControllerIntegrationTest.java
+++ b/src/test/java/org/breedinginsight/brapi/v2/BrAPIStudiesControllerIntegrationTest.java
@@ -335,7 +335,7 @@ private String getEnvId(JsonObject result, int index) {
                 .get("brAPIObject").getAsJsonObject()
                 .get("externalReferences").getAsJsonArray()
                 .get(2).getAsJsonObject()
-                .get("referenceID").getAsString();
+                .get("referenceId").getAsString();
     }
 
     private List<BrAPIGermplasm> createGermplasm(int numToCreate) {
diff --git a/src/test/java/org/breedinginsight/brapi/v2/BrAPIV2ObservationVariableControllerIntegrationTest.java b/src/test/java/org/breedinginsight/brapi/v2/BrAPIV2ObservationVariableControllerIntegrationTest.java
index 58c20194f..79056913e 100644
--- a/src/test/java/org/breedinginsight/brapi/v2/BrAPIV2ObservationVariableControllerIntegrationTest.java
+++ b/src/test/java/org/breedinginsight/brapi/v2/BrAPIV2ObservationVariableControllerIntegrationTest.java
@@ -156,7 +156,7 @@ void setup() throws Exception {
         List<BrAPIGermplasm> germplasm = createGermplasm(1);
         BrAPIExternalReference newReference = new BrAPIExternalReference();
         newReference.setReferenceSource(String.format("%s/programs", BRAPI_REFERENCE_SOURCE));
-        newReference.setReferenceID(program.getId().toString());
+        newReference.setReferenceId(program.getId().toString());
 
         germplasm.forEach(germ -> germ.getExternalReferences().add(newReference));
 
@@ -344,7 +344,7 @@ private String getEnvId(JsonObject result, int index) {
                 .get("brAPIObject").getAsJsonObject()
                 .get("externalReferences").getAsJsonArray()
                 .get(2).getAsJsonObject()
-                .get("referenceID").getAsString();
+                .get("referenceId").getAsString();
     }
 
     private List<BrAPIGermplasm> createGermplasm(int numToCreate) {
@@ -363,7 +363,7 @@ private List<BrAPIGermplasm> createGermplasm(int numToCreate) {
             List<BrAPIExternalReference> externalRef = new ArrayList<>();
             BrAPIExternalReference testReference = new BrAPIExternalReference();
             testReference.setReferenceSource(BRAPI_REFERENCE_SOURCE);
-            testReference.setReferenceID(UUID.randomUUID().toString());
+            testReference.setReferenceId(UUID.randomUUID().toString());
             externalRef.add(testReference);
             testGermplasm.setExternalReferences(externalRef);
             germplasm.add(testGermplasm);
diff --git a/src/test/java/org/breedinginsight/brapi/v2/ExperimentControllerIntegrationTest.java b/src/test/java/org/breedinginsight/brapi/v2/ExperimentControllerIntegrationTest.java
index 630c29c85..80c281c39 100644
--- a/src/test/java/org/breedinginsight/brapi/v2/ExperimentControllerIntegrationTest.java
+++ b/src/test/java/org/breedinginsight/brapi/v2/ExperimentControllerIntegrationTest.java
@@ -14,6 +14,7 @@
 import lombok.SneakyThrows;
 import org.apache.commons.io.FileUtils;
 import org.brapi.v2.model.BrAPIExternalReference;
+import org.brapi.v2.model.core.BrAPITrial;
 import org.brapi.v2.model.germ.BrAPIGermplasm;
 import org.breedinginsight.BrAPITest;
 import org.breedinginsight.TestUtils;
@@ -22,6 +23,7 @@
 import org.breedinginsight.api.model.v1.request.SpeciesRequest;
 import org.breedinginsight.api.v1.controller.TestTokenValidator;
 import org.breedinginsight.brapi.v2.dao.BrAPIGermplasmDAO;
+import org.breedinginsight.brapi.v2.services.BrAPITrialService;
 import org.breedinginsight.brapps.importer.ImportTestUtils;
 import org.breedinginsight.brapps.importer.model.exports.FileType;
 import org.breedinginsight.brapps.importer.model.imports.experimentObservation.ExperimentObservation;
@@ -35,6 +37,7 @@
 import org.breedinginsight.services.parsers.ParsingException;
 import org.breedinginsight.services.parsers.experiment.ExperimentFileColumns;
 import org.breedinginsight.services.writers.CSVWriter;
+import org.breedinginsight.utilities.DatasetUtil;
 import org.breedinginsight.utilities.FileUtil;
 import org.jooq.DSLContext;
 import org.junit.jupiter.api.*;
@@ -74,6 +77,8 @@ public class ExperimentControllerIntegrationTest extends BrAPITest {
     @Inject
     private OntologyService ontologyService;
     @Inject
+    private BrAPITrialService experimentService;
+    @Inject
     private BrAPIGermplasmDAO germplasmDAO;
 
     @Inject
@@ -209,6 +214,11 @@ void setup() throws Exception {
             "true,XLSX,2", "false,XLSX,2",})
     @SneakyThrows
     void downloadDatasets(boolean includeTimestamps, String extension, int numberOfEnvsRequested) {
+        // How many columns are expected in the output?
+        int expectedColNumber = columns.size();
+        if (includeTimestamps) {
+            expectedColNumber += traits.size();
+        }
         // Temporary directory to extract zip into, test will clean up after use.
         String tempDir = "./zip_temp_dir/";
         // If more than 1 envId is sent as a query param, a zip file is expected response.
@@ -220,9 +230,11 @@ void downloadDatasets(boolean includeTimestamps, String extension, int numberOfE
             String envs = numberOfEnvsRequested == 1 ? envIds.get(0) : String.join(",", envIds);
             envParam = "environments=" + envs;
         }
+        // Get datasetId to include in export request.
+        String datasetId = experimentService.getDatasetsMetadata(program, UUID.fromString(experimentId)).stream().findFirst().get().getId().toString();
         Flowable<HttpResponse<byte[]>> call = client.exchange(
-                GET(String.format("/programs/%s/experiments/%s/export?includeTimestamps=%s&%s&fileExtension=%s",
-                        program.getId().toString(), experimentId, includeTimestamps, envParam, extension))
+                GET(String.format("/programs/%s/experiments/%s/export?includeTimestamps=%s&%s&fileExtension=%s&datasetId=%s",
+                        program.getId().toString(), experimentId, includeTimestamps, envParam, extension, datasetId))
                         .cookie(new NettyCookie("phylo-token", "test-registered-user")), byte[].class
         );
         HttpResponse<byte[]> response = call.blockingFirst();
@@ -251,20 +263,105 @@ void downloadDatasets(boolean includeTimestamps, String extension, int numberOfE
                 List<Map<String, Object>> filteredRows = rows.stream()
                         .filter(row -> file.getName().contains(row.get(ExperimentObservation.Columns.ENV).toString()))
                         .collect(Collectors.toList());
-                parseAndCheck(fileStream, extension, true, filteredRows, includeTimestamps);
+                parseAndCheck(fileStream, extension, true, filteredRows, includeTimestamps, expectedColNumber);
             }
         }
         else {
             assertEquals(mediaTypeByExtension.get(extension), downloadMediaType);
             // All (both) rows when 0 or 2 envs sent, first row when 1 env sent as query param.
             List<Map<String, Object>> filteredRows = numberOfEnvsRequested == 1 ? List.of(rows.get(0)) : rows;
-            parseAndCheck(bodyStream, extension, numberOfEnvsRequested > 0, filteredRows, includeTimestamps);
-
+            parseAndCheck(bodyStream, extension, numberOfEnvsRequested > 0, filteredRows, includeTimestamps, expectedColNumber);
         }
         // Remove temp directory after each test run.
         FileUtils.deleteDirectory(new File(tempDir));
     }
 
+    /**
+     * Tests creating and subsequently downloading a sub-entity dataset.
+     * It also ensures no regressions with the top-level dataset download are introduced by the sub-entity features.
+     */
+    @ParameterizedTest
+    @CsvSource(value = {"CSV", "XLSX", "XLS"})
+    @SneakyThrows
+    void downloadSubEntityDataset(String extension) {
+
+        // Create sub-entity dataset.
+        Flowable<HttpResponse<byte[]>> postCall = client.exchange(
+                POST(String.format("/programs/%s/experiments/%s/dataset",
+                                program.getId().toString(), experimentId),
+                        "{\"name\":\"Plant\",\"repeatedMeasures\":3}")
+                        .cookie(new NettyCookie("phylo-token", "test-registered-user")),
+                byte[].class);
+        HttpResponse<byte[]> postResponse = postCall.blockingFirst();
+
+        // Assert 200 response
+        assertEquals(HttpStatus.OK, postResponse.getStatus());
+
+        // Get top-level datasetId to include in export request.
+        BrAPITrial experiment = experimentService.getTrialDataByUUID(program.getId(), UUID.fromString(experimentId), false);
+        String topLevelDatasetId = DatasetUtil.getTopLevelDataset(experiment).getId().toString();
+        Flowable<HttpResponse<byte[]>> topLevelExportCall = client.exchange(
+                GET(String.format("/programs/%s/experiments/%s/export?all=true&includeTimestamps=false&fileExtension=%s&datasetId=%s",
+                        program.getId().toString(), experimentId, extension, topLevelDatasetId))
+                        .cookie(new NettyCookie("phylo-token", "test-registered-user")), byte[].class
+        );
+        HttpResponse<byte[]> topLevelResponse = topLevelExportCall.blockingFirst();
+
+        // Assert 200 response
+        assertEquals(HttpStatus.OK, topLevelResponse.getStatus());
+
+        // Assert file format fidelity
+        Map<String, String> mediaTypeByExtension = new HashMap<>();
+        mediaTypeByExtension.put("CSV", FileType.CSV.getMimeType());
+        mediaTypeByExtension.put("XLS", FileType.XLS.getMimeType());
+        mediaTypeByExtension.put("XLSX", FileType.XLSX.getMimeType());
+        String downloadMediaType = topLevelResponse.getHeaders().getContentType().orElseThrow(Exception::new);
+        assertEquals(mediaTypeByExtension.get(extension), downloadMediaType);
+
+        // Check file contents.
+        ByteArrayInputStream bodyStream = new ByteArrayInputStream(Objects.requireNonNull(topLevelResponse.body()));
+        parseAndCheck(bodyStream, extension, false, rows, false, 25);
+
+        // Make sub-entity dataset export request.
+        String plantDatasetId = DatasetUtil.getDatasetIdByNameFromJson(experiment.getAdditionalInfo().getAsJsonArray("datasets"), "Plant");
+        Flowable<HttpResponse<byte[]>> plantExportCall = client.exchange(
+                GET(String.format("/programs/%s/experiments/%s/export?all=true&includeTimestamps=false&fileExtension=%s&datasetId=%s",
+                        program.getId().toString(), experimentId, extension, plantDatasetId))
+                        .cookie(new NettyCookie("phylo-token", "test-registered-user")), byte[].class
+        );
+        HttpResponse<byte[]> plantResponse = plantExportCall.blockingFirst();
+
+        // Assert 200 response
+        assertEquals(HttpStatus.OK, plantResponse.getStatus());
+
+        // Assert file format fidelity
+        assertEquals(mediaTypeByExtension.get(extension), plantResponse.getHeaders().getContentType().orElseThrow(Exception::new));
+
+        // The expected contents of the exported Plant dataset (3 sub-obs units for each top-level unit were requested).
+        List<Map<String, Object>> plantRows = buildSubEntityRows(rows, "Plant", 3);
+
+        // Check file contents.
+        ByteArrayInputStream plantBodyStream = new ByteArrayInputStream(Objects.requireNonNull(plantResponse.body()));
+        parseAndCheck(plantBodyStream, extension, false, plantRows, false, 23);
+    }
+
+    private List<Map<String, Object>> buildSubEntityRows(List<Map<String, Object>> topLevelRows, String entityName, int repeatedMeasures) {
+        List<Map<String, Object>> plantRows = new ArrayList<>();
+        for (Map<String, Object> row : topLevelRows) {
+            for (Integer i=1; i<=repeatedMeasures; i++) {
+                // Deep copy map entries.
+                Map<String, Object> plantRow = new HashMap<>(row);
+
+                plantRow.put("Exp Unit", entityName);
+                plantRow.put("Exp Unit ID", i.toString());
+                plantRow.remove("tt_test_1");
+                plantRow.remove("tt_test_2");
+                plantRows.add(plantRow);
+            }
+        }
+        return plantRows;
+    }
+
     private File writeDataToFile(List<Map<String, Object>> data, List<Trait> traits) throws IOException {
         File file = File.createTempFile("test", ".csv");
 
@@ -364,7 +461,8 @@ private void parseAndCheck(InputStream stream,
                                String extension,
                                boolean requestEnv,
                                List<Map<String, Object>> rows,
-                               boolean includeTimestamps) throws ParsingException {
+                               boolean includeTimestamps,
+                               Integer expectedColNumber) throws ParsingException {
         Table download = Table.create();
         if (extension.equals("CSV")) {
             download = FileUtil.parseTableFromCsv(stream);
@@ -372,8 +470,9 @@ private void parseAndCheck(InputStream stream,
         if (extension.equals("XLS") || extension.equals("XLSX")) {
             download = FileUtil.parseTableFromExcel(stream, 0);
         }
+
         // Assert import/export fidelity and presence of observation units in export
-        checkDownloadTable(requestEnv, rows, download, includeTimestamps, extension);
+        checkDownloadTable(requestEnv, rows, download, includeTimestamps, extension, expectedColNumber);
     }
 
     private void checkDownloadTable(
@@ -381,15 +480,12 @@ private void checkDownloadTable(
             List<Map<String, Object>> requestedImportRows,
             Table table,
             boolean includeTimestamps,
-            String extension) {
+            String extension,
+            Integer expectedColNumber) {
         // Filename is correct: <exp-title>_Observation Dataset [<prog-key>-<exp-seq>]_<environment>_<export-timestamp>
         List<String> expectedEnvNames = requestedImportRows.stream()
                 .map(row -> row.get(ExperimentObservation.Columns.ENV).toString()).collect(Collectors.toList());
-        // All columns included
-        Integer expectedColNumber = columns.size();
-        if (includeTimestamps) {
-            expectedColNumber += traits.size();
-        }
+
         assertEquals(expectedColNumber, table.columnCount());
 
         // Check that requested envs are present.
@@ -402,15 +498,19 @@ private void checkDownloadTable(
             Row downloadRow = table.row(rowNum);
 
             // sort order is not guaranteed to be th same as import, so find import row for corresponding export row
-            // by first matching environment and GID
+            // by first matching environment, GID and Exp Unit ID
             matchingImportRow = requestedImportRows.stream().filter(row -> {
                 String gid = ExperimentObservation.Columns.GERMPLASM_GID;
                 String env = ExperimentObservation.Columns.ENV;
+                String expUnitId = ExperimentObservation.Columns.EXP_UNIT_ID;
                 if (extension.equalsIgnoreCase(FileType.CSV.getName())) {
                     return Integer.parseInt(row.get(gid).toString()) == downloadRow.getInt(gid) &&
-                            row.get(env).equals(downloadRow.getString(env));
+                            row.get(env).equals(downloadRow.getString(env)) &&
+                            row.get(expUnitId).equals(downloadRow.getObject(expUnitId).toString());
                 } else {
-                    return row.get(gid).equals(downloadRow.getString(gid)) && row.get(env).equals(downloadRow.getString(env));
+                    return row.get(gid).equals(downloadRow.getString(gid)) &&
+                            row.get(env).equals(downloadRow.getString(env)) &&
+                            row.get(expUnitId).equals(downloadRow.getObject(expUnitId).toString());
                 }
             }).findAny();
             assertTrue(matchingImportRow.isPresent() && !matchingImportRow.get().isEmpty());
@@ -482,7 +582,7 @@ private String getEnvId(JsonObject result, int index) {
                 .get("brAPIObject").getAsJsonObject()
                 .get("externalReferences").getAsJsonArray()
                 .get(2).getAsJsonObject()
-                .get("referenceID").getAsString();
+                .get("referenceId").getAsString();
     }
 
 }
diff --git a/src/test/java/org/breedinginsight/brapps/importer/ExperimentFileImportTest.java b/src/test/java/org/breedinginsight/brapps/importer/ExperimentFileImportTest.java
index 48bffd4c2..2dda40e60 100644
--- a/src/test/java/org/breedinginsight/brapps/importer/ExperimentFileImportTest.java
+++ b/src/test/java/org/breedinginsight/brapps/importer/ExperimentFileImportTest.java
@@ -446,10 +446,11 @@ public void importNewExpWithObsVar() {
         JsonArray previewRows = result.get("preview").getAsJsonObject().get("rows").getAsJsonArray();
         assertEquals(1, previewRows.size());
         JsonObject row = previewRows.get(0).getAsJsonObject();
+        JsonArray datasets = row.getAsJsonObject("trial").get("brAPIObject").getAsJsonObject().get("additionalInfo").getAsJsonObject().getAsJsonArray(BrAPIAdditionalInfoFields.DATASETS);
 
         assertEquals("NEW", row.getAsJsonObject("trial").get("state").getAsString());
-        assertTrue(row.getAsJsonObject("trial").get("brAPIObject").getAsJsonObject().get("additionalInfo").getAsJsonObject().has("observationDatasetId"));
-        assertTrue(importTestUtils.UUID_REGEX.matcher(row.getAsJsonObject("trial").get("brAPIObject").getAsJsonObject().get("additionalInfo").getAsJsonObject().get("observationDatasetId").getAsString()).matches());
+        assertFalse(datasets.isEmpty());
+        assertTrue(importTestUtils.UUID_REGEX.matcher(datasets.get(0).getAsJsonObject().get("id").getAsString()).matches());
         assertEquals("NEW", row.getAsJsonObject("location").get("state").getAsString());
         assertEquals("NEW", row.getAsJsonObject("study").get("state").getAsString());
         assertEquals("NEW", row.getAsJsonObject("observationUnit").get("state").getAsString());
@@ -691,10 +692,11 @@ public void importNewObsVarExistingOu() {
         JsonArray previewRows = result.get("preview").getAsJsonObject().get("rows").getAsJsonArray();
         assertEquals(1, previewRows.size());
         JsonObject row = previewRows.get(0).getAsJsonObject();
+        JsonArray datasets = row.getAsJsonObject("trial").get("brAPIObject").getAsJsonObject().get("additionalInfo").getAsJsonObject().getAsJsonArray(BrAPIAdditionalInfoFields.DATASETS);
 
         assertEquals("EXISTING", row.getAsJsonObject("trial").get("state").getAsString());
-        assertTrue(row.getAsJsonObject("trial").get("brAPIObject").getAsJsonObject().get("additionalInfo").getAsJsonObject().has("observationDatasetId"));
-        assertTrue(importTestUtils.UUID_REGEX.matcher(row.getAsJsonObject("trial").get("brAPIObject").getAsJsonObject().get("additionalInfo").getAsJsonObject().get("observationDatasetId").getAsString()).matches());
+        assertFalse(datasets.isEmpty());
+        assertTrue(importTestUtils.UUID_REGEX.matcher(datasets.get(0).getAsJsonObject().get("id").getAsString()).matches());
         assertEquals("EXISTING", row.getAsJsonObject("location").get("state").getAsString());
         assertEquals("EXISTING", row.getAsJsonObject("study").get("state").getAsString());
         assertEquals("EXISTING", row.getAsJsonObject("observationUnit").get("state").getAsString());
@@ -742,10 +744,11 @@ public void importNewObsVarByObsUnitId() {
         JsonArray previewRows = result.get("preview").getAsJsonObject().get("rows").getAsJsonArray();
         assertEquals(1, previewRows.size());
         JsonObject row = previewRows.get(0).getAsJsonObject();
+        JsonArray datasets = row.getAsJsonObject("trial").get("brAPIObject").getAsJsonObject().get("additionalInfo").getAsJsonObject().getAsJsonArray(BrAPIAdditionalInfoFields.DATASETS);
 
         assertEquals("EXISTING", row.getAsJsonObject("trial").get("state").getAsString());
-        assertTrue(row.getAsJsonObject("trial").get("brAPIObject").getAsJsonObject().get("additionalInfo").getAsJsonObject().has("observationDatasetId"));
-        assertTrue(importTestUtils.UUID_REGEX.matcher(row.getAsJsonObject("trial").get("brAPIObject").getAsJsonObject().get("additionalInfo").getAsJsonObject().get("observationDatasetId").getAsString()).matches());
+        assertFalse(datasets.isEmpty());
+        assertTrue(importTestUtils.UUID_REGEX.matcher(datasets.get(0).getAsJsonObject().get("id").getAsString()).matches());
         assertEquals("EXISTING", row.getAsJsonObject("location").get("state").getAsString());
         assertEquals("EXISTING", row.getAsJsonObject("study").get("state").getAsString());
         assertEquals("EXISTING", row.getAsJsonObject("observationUnit").get("state").getAsString());
@@ -807,10 +810,11 @@ public void importNewObservationDataByObsUnitId(boolean commit) {
         JsonArray previewRows = result.get("preview").getAsJsonObject().get("rows").getAsJsonArray();
         assertEquals(1, previewRows.size());
         JsonObject row = previewRows.get(0).getAsJsonObject();
+        JsonArray datasets = row.getAsJsonObject("trial").get("brAPIObject").getAsJsonObject().get("additionalInfo").getAsJsonObject().getAsJsonArray(BrAPIAdditionalInfoFields.DATASETS);
 
         assertEquals("EXISTING", row.getAsJsonObject("trial").get("state").getAsString());
-        assertTrue(row.getAsJsonObject("trial").get("brAPIObject").getAsJsonObject().get("additionalInfo").getAsJsonObject().has("observationDatasetId"));
-        assertTrue(importTestUtils.UUID_REGEX.matcher(row.getAsJsonObject("trial").get("brAPIObject").getAsJsonObject().get("additionalInfo").getAsJsonObject().get("observationDatasetId").getAsString()).matches());
+        assertFalse(datasets.isEmpty());
+        assertTrue(importTestUtils.UUID_REGEX.matcher(datasets.get(0).getAsJsonObject().get("id").getAsString()).matches());
         assertEquals("EXISTING", row.getAsJsonObject("location").get("state").getAsString());
         assertEquals("EXISTING", row.getAsJsonObject("study").get("state").getAsString());
         assertEquals("EXISTING", row.getAsJsonObject("observationUnit").get("state").getAsString());