diff --git a/manim/scene/scene.py b/manim/scene/scene.py
index 44282df581..c8c6bc9362 100644
--- a/manim/scene/scene.py
+++ b/manim/scene/scene.py
@@ -218,6 +218,37 @@ def remove(self, *mobjects_to_remove: OpenGLMobject) -> Self:
             self.mobjects = list_difference_update(self.mobjects, mob.get_family())
         return self
 
+    def _replace(
+        self,
+        parent_mobjects: list[OpenGLMobject],
+        mobject: OpenGLMobject,
+        *replacements: OpenGLMobject,
+    ) -> list[OpenGLMobject]:
+        """Replace one Mobject in a parent Mobject with one or more other Mobjects,
+        preserving draw order.
+
+        Parameters
+        ----------
+        pareparent_mobjectsnt
+            The parent mobjects list where the mobject is going to be replaced
+        mobject
+            The mobject to be replaced. Must be present in the scene.
+        replacements
+            One or more Mobjects which must not already be in the scene.
+        """
+        if mobject in parent_mobjects:
+            index = parent_mobjects.index(mobject)
+            parent_mobjects = [
+                *parent_mobjects[:index],
+                *[
+                    replacement
+                    for replacement in replacements
+                    if replacement not in parent_mobjects
+                ],
+                *parent_mobjects[index + 1 :],
+            ]
+        return parent_mobjects
+
     def replace(self, mobject: OpenGLMobject, *replacements: OpenGLMobject):
         """Replace one Mobject in the scene with one or more other Mobjects,
         preserving draw order.
@@ -234,17 +265,13 @@ def replace(self, mobject: OpenGLMobject, *replacements: OpenGLMobject):
             One or more Mobjects which must not already be in the scene.
 
         """
-        if mobject in self.mobjects:
-            index = self.mobjects.index(mobject)
-            self.mobjects = [
-                *self.mobjects[:index],
-                *[
-                    replacement
-                    for replacement in replacements
-                    if replacement not in self.mobjects
-                ],
-                *self.mobjects[index + 1 :],
-            ]
+        for ancestor in mobject.get_ancestors():
+            ancestor.submobjects = self._replace(
+                ancestor.submobjects, mobject, *replacements
+            )
+
+        self.mobjects = self._replace(self.mobjects, mobject, *replacements)
+
         return self
 
     def add_updater(self, func: Callable[[float], None]) -> None:
diff --git a/tests/module/animation/test_transform.py b/tests/module/animation/test_transform.py
index 1e452857fd..6600c3632e 100644
--- a/tests/module/animation/test_transform.py
+++ b/tests/module/animation/test_transform.py
@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from manim import Circle, Manager, ReplacementTransform, Scene, Square, VGroup
+from manim import Circle, Manager, ReplacementTransform, Scene, Square, Triangle, VGroup
 
 
 def test_no_duplicate_references():
@@ -27,3 +27,23 @@ def test_duplicate_references_in_group():
     submobs = vg.submobjects
     assert len(submobs) == 1
     assert submobs[0] is sq
+
+
+def test_duplicate_references_in_multiple_groups():
+    manager = Manager(Scene)
+    scene = manager.scene
+    c = Circle()
+    sq = Square()
+    tr = Triangle()
+    vg_1 = VGroup(c, sq)
+    vg_2 = VGroup(c, tr)
+    scene.add(vg_1, vg_2)
+
+    scene.play(ReplacementTransform(c, sq))
+    submobs_1 = vg_1.submobjects
+    submobs_2 = vg_2.submobjects
+    assert len(submobs_1) == 1
+    assert submobs_1[0] is sq
+    assert len(submobs_2) == 2
+    assert submobs_2[0] is sq
+    assert submobs_2[1] is tr