diff --git a/dd-java-agent/agent-bootstrap/src/main/java/datadog/trace/bootstrap/AgentJarIndex.java b/dd-java-agent/agent-bootstrap/src/main/java/datadog/trace/bootstrap/AgentJarIndex.java
index 382f8708ac6..168c916d994 100644
--- a/dd-java-agent/agent-bootstrap/src/main/java/datadog/trace/bootstrap/AgentJarIndex.java
+++ b/dd-java-agent/agent-bootstrap/src/main/java/datadog/trace/bootstrap/AgentJarIndex.java
@@ -142,6 +142,12 @@ public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) {
       if (null != prefixRoot) {
         String entryKey = computeEntryKey(prefixRoot.relativize(file));
         if (null != entryKey) {
+          int existingPrefixId = prefixTrie.apply(entryKey);
+          if (-1 != existingPrefixId && prefixId != existingPrefixId) {
+            log.warn(
+                "Detected duplicate content under '{}'. Ensure your content is under a distinct directory.",
+                entryKey);
+          }
           prefixTrie.put(entryKey, prefixId);
           if (entryKey.endsWith("*")) {
             // optimization: wildcard will match everything under here so can skip