diff --git a/package/CHANGELOG b/package/CHANGELOG
index 0ed734f69c2..b868514676d 100644
--- a/package/CHANGELOG
+++ b/package/CHANGELOG
@@ -23,6 +23,8 @@ The rules for this file:
   * 2.0.0
 
 Fixes
+  * Fixed MDAnalysis.analysis.align.alignto to reindex given mobile and 
+    reference atoms before passing for alignment (issue #2977)
   * Only GRO files with unit cells defined with 3 or 9 entries are now
     supported (Issue #3305)
   * Ensures that reading and writing of GRO files with missing unit cell
diff --git a/package/MDAnalysis/analysis/align.py b/package/MDAnalysis/analysis/align.py
index d03656f0490..672a0b1c772 100644
--- a/package/MDAnalysis/analysis/align.py
+++ b/package/MDAnalysis/analysis/align.py
@@ -482,8 +482,8 @@ def alignto(mobile, reference, select=None, weights=None,
         ref_atoms = reference.atoms
     else:
         select = rms.process_selection(select)
-        mobile_atoms = mobile.select_atoms(*select['mobile'])
-        ref_atoms = reference.select_atoms(*select['reference'])
+        mobile_atoms = mobile.select_atoms(*select['mobile']).sort()
+        ref_atoms = reference.select_atoms(*select['reference']).sort()
 
 
     ref_atoms, mobile_atoms = get_matching_atoms(ref_atoms, mobile_atoms,
diff --git a/testsuite/MDAnalysisTests/analysis/test_align.py b/testsuite/MDAnalysisTests/analysis/test_align.py
index 6edc0ac8fa9..7435fd1fa9f 100644
--- a/testsuite/MDAnalysisTests/analysis/test_align.py
+++ b/testsuite/MDAnalysisTests/analysis/test_align.py
@@ -395,6 +395,12 @@ def test_alignto_partial_universe(self, universe, reference):
         assert_array_almost_equal(segB_bound.positions, segB_free.positions,
                                   decimal=3)
 
+    def test_alignto_sort(self, universe):
+        mobile = universe.atoms[:4]
+        ref = universe.atoms[[3, 2, 1, 0]]
+        np.testing.assert_allclose(align.alignto(mobile, ref,
+                                   select='bynum 1-4'), (0.0, 0.0))
+
 
 def _get_aligned_average_positions(ref_files, ref, select="all", **kwargs):
     u = mda.Universe(*ref_files, in_memory=True)