diff --git a/package/AUTHORS b/package/AUTHORS
index e8e41573d9..4cd9d75a3a 100644
--- a/package/AUTHORS
+++ b/package/AUTHORS
@@ -280,6 +280,7 @@ Chronological list of authors
   - Amarendra Mohan
   - Shubham Mittal  
   - Charity Grey
+  - Dhanushka Weerakoon
 
 External code
 -------------
diff --git a/package/CHANGELOG b/package/CHANGELOG
index fd0b869186..9edcd0b45e 100644
--- a/package/CHANGELOG
+++ b/package/CHANGELOG
@@ -17,11 +17,13 @@ The rules for this file:
 ??/??/?? IAlibay, orbeckst, marinegor, tylerjereddy, ljwoods2, marinegor,
          spyke7, talagayev, tanii1125, BradyAJohnston, hejamu, jeremyleung521,
          harshitgajjela-droid, kunjsinha, aygarwal, jauy123, Dreamstick9,
-         ollyfutur, Amarendra22, charity-g, ParthUppal523
+         ollyfutur, Amarendra22, charity-g, ParthUppal523, DhanushkaWeerakoon
 
  * 2.11.0
 
 Fixes
+* Fix mismatch in target and reference groupselection coordinates which
+   can occur during RMSD calculations (Issue #2797) 
  * `MDAnalysis.analysis.nucleicacids.WatsonCrickDist`, `MinorPairDist`,
    and `MajorPairDist` now match residue names against the full resname
    instead of only the first character, fixing incorrect behaviour with
diff --git a/package/MDAnalysis/analysis/rms.py b/package/MDAnalysis/analysis/rms.py
index 4b76723e7b..54dac2c0ff 100644
--- a/package/MDAnalysis/analysis/rms.py
+++ b/package/MDAnalysis/analysis/rms.py
@@ -733,7 +733,7 @@ def _prepare(self):
             if self._groupselections_atoms:
                 self._groupselections_ref_coords64 = [
                     (
-                        self.reference.select_atoms(
+                        self.reference.universe.select_atoms(
                             *s["reference"]
                         ).positions.astype(np.float64)
                     )
diff --git a/testsuite/MDAnalysisTests/analysis/test_rms.py b/testsuite/MDAnalysisTests/analysis/test_rms.py
index 9479c96ead..48c13fc670 100644
--- a/testsuite/MDAnalysisTests/analysis/test_rms.py
+++ b/testsuite/MDAnalysisTests/analysis/test_rms.py
@@ -194,6 +194,10 @@ def correct_values_group(self):
     def correct_values_backbone_group(self):
         return [[0, 1, 0, 0, 0], [49, 50, 4.6997, 1.9154, 2.7139]]
 
+    @pytest.fixture()
+    def correct_values_alphacarbons_group(self):
+        return [[0, 1, 0, 0], [49, 50, 1.6521, 1.6371]]
+
     def test_rmsd(self, universe, correct_values, client_RMSD):
         # client_RMSD is defined in testsuite/analysis/conftest.py
         # among with other testing fixtures. During testing, it will
@@ -509,6 +513,30 @@ def test_rmsd_misuse_selec_raises_TypeError(self, universe):
                 select=42,
             )
 
+    def test_group_selections_outside_atomgroup(
+            self,
+            universe,
+            correct_values_alphacarbons_group,
+            client_RMSD
+            ):
+        ca = universe.select_atoms('name CA')
+        CORE = 'backbone and (resid 1-29 or resid 60-121 or resid 160-214)'
+        RMSD = MDAnalysis.analysis.rms.RMSD(
+            ca,
+            ca,
+            select=CORE,
+            groupselections=[CORE],
+        )
+        RMSD.run(step=49, **client_RMSD)
+
+        assert_almost_equal(
+            RMSD.results.rmsd,
+            correct_values_alphacarbons_group,
+            4,
+            err_msg="error: rmsd profile should match"
+            "between true values and calculated values"
+        )
+
 
 class TestRMSF(object):
     @pytest.fixture()