diff --git a/django/db/migrations/autodetector.py b/django/db/migrations/autodetector.py
index 4bcbae8bd38..ad324376307 100644
--- a/django/db/migrations/autodetector.py
+++ b/django/db/migrations/autodetector.py
@@ -189,14 +189,14 @@ class MigrationAutodetector:
         self.generate_renamed_indexes()
         # Generate removal of foo together.
         self.generate_removed_altered_unique_together()
-        self.generate_removed_altered_index_together()
+        self.generate_removed_altered_index_together()  # RemovedInDjango51Warning.
         # Generate field operations.
         self.generate_removed_fields()
         self.generate_added_fields()
         self.generate_altered_fields()
         self.generate_altered_order_with_respect_to()
         self.generate_altered_unique_together()
-        self.generate_altered_index_together()
+        self.generate_altered_index_together()  # RemovedInDjango51Warning.
         self.generate_added_indexes()
         self.generate_added_constraints()
         self.generate_altered_db_table()
@@ -616,6 +616,7 @@ class MigrationAutodetector:
             indexes = model_state.options.pop("indexes")
             constraints = model_state.options.pop("constraints")
             unique_together = model_state.options.pop("unique_together", None)
+            # RemovedInDjango51Warning.
             index_together = model_state.options.pop("index_together", None)
             order_with_respect_to = model_state.options.pop(
                 "order_with_respect_to", None
@@ -745,6 +746,7 @@ class MigrationAutodetector:
                     ),
                     dependencies=related_dependencies,
                 )
+            # RemovedInDjango51Warning.
             if index_together:
                 self.add_operation(
                     app_label,
@@ -834,6 +836,7 @@ class MigrationAutodetector:
                         related_fields[field_name] = field
             # Generate option removal first
             unique_together = model_state.options.pop("unique_together", None)
+            # RemovedInDjango51Warning.
             index_together = model_state.options.pop("index_together", None)
             if unique_together:
                 self.add_operation(
@@ -843,6 +846,7 @@ class MigrationAutodetector:
                         unique_together=None,
                     ),
                 )
+            # RemovedInDjango51Warning.
             if index_together:
                 self.add_operation(
                     app_label,
@@ -1500,6 +1504,7 @@ class MigrationAutodetector:
     def generate_removed_altered_unique_together(self):
         self._generate_removed_altered_foo_together(operations.AlterUniqueTogether)
 
+    # RemovedInDjango51Warning.
     def generate_removed_altered_index_together(self):
         self._generate_removed_altered_foo_together(operations.AlterIndexTogether)
 
@@ -1522,6 +1527,7 @@ class MigrationAutodetector:
     def generate_altered_unique_together(self):
         self._generate_altered_foo_together(operations.AlterUniqueTogether)
 
+    # RemovedInDjango51Warning.
     def generate_altered_index_together(self):
         self._generate_altered_foo_together(operations.AlterIndexTogether)
 
diff --git a/django/db/models/base.py b/django/db/models/base.py
index 69224c02870..04f045d9238 100644
--- a/django/db/models/base.py
+++ b/django/db/models/base.py
@@ -1841,6 +1841,7 @@ class Model(metaclass=ModelBase):
             )
         return errors
 
+    # RemovedInDjango51Warning.
     @classmethod
     def _check_index_together(cls):
         """Check the value of "index_together" option."""
diff --git a/django/db/models/options.py b/django/db/models/options.py
index 938b996d67b..bff55011dc8 100644
--- a/django/db/models/options.py
+++ b/django/db/models/options.py
@@ -42,6 +42,7 @@ DEFAULT_NAMES = (
     "proxy",
     "swappable",
     "auto_created",
+    # Must be kept for backward compatibility with old migrations.
     "index_together",
     "apps",
     "default_permissions",
@@ -115,7 +116,7 @@ class Options:
         self.indexes = []
         self.constraints = []
         self.unique_together = []
-        self.index_together = []
+        self.index_together = []  # RemovedInDjango51Warning.
         self.select_on_save = False
         self.default_permissions = ("add", "change", "delete", "view")
         self.permissions = []
diff --git a/tests/migrations/test_operations.py b/tests/migrations/test_operations.py
index d60f5cd1833..8c7edac4782 100644
--- a/tests/migrations/test_operations.py
+++ b/tests/migrations/test_operations.py
@@ -2491,7 +2491,6 @@ class OperationTests(OperationTestBase):
             atomic=connection.features.supports_atomic_references_rename,
         )
 
-    @ignore_warnings(category=RemovedInDjango51Warning)
     def test_rename_field(self):
         """
         Tests the RenameField operation.