diff --git a/petab/v2/lint.py b/petab/v2/lint.py
index 80f47b04..5748e52b 100644
--- a/petab/v2/lint.py
+++ b/petab/v2/lint.py
@@ -945,8 +945,8 @@ def run(self, problem: Problem) -> ValidationIssue | None:
         new_petab_ids = {
             m.petab_id
             for m in problem.mappings
-            # Ignore identity mappings used for annotation
-            if m.petab_id != m.model_id
+            # Ignore identity mappings and annotation-only rows
+            if m.model_id and m.petab_id != m.model_id
         }
         old_petab_ids = (
             {c.id for c in problem.conditions}
diff --git a/tests/v2/test_lint.py b/tests/v2/test_lint.py
index aae8a5e4..65d4796f 100644
--- a/tests/v2/test_lint.py
+++ b/tests/v2/test_lint.py
@@ -146,6 +146,14 @@ def test_check_mapping_table(uses_pysb):
     check = CheckMappingTable()
     assert check.run(problem) is None
 
+    # Valid: mapping table is used purely for annotation
+    # petabEntityId appears elsewhere in the problem
+    problem.add_mapping(petab_id="c1", model_id=None, name="Condition 1")
+    problem.add_condition("c1", p2="1")
+
+    check = CheckMappingTable()
+    assert check.run(problem) is None
+
     # Invalid: petabEntityId is referenced in the model
     pysb.SelfExporter.cleanup()
     pysb_model_invalid = pysb.Model("test_model_invalid")