diff --git a/packages/linkml/src/linkml/generators/owlgen.py b/packages/linkml/src/linkml/generators/owlgen.py
index 33c58b0ec..3f4eb4c18 100644
--- a/packages/linkml/src/linkml/generators/owlgen.py
+++ b/packages/linkml/src/linkml/generators/owlgen.py
@@ -201,7 +201,11 @@ class OwlSchemaGenerator(Generator):
     one direct ``is_a`` child, the generator adds
     ``AbstractClass rdfs:subClassOf (Child1 or Child2 or …)``, expressing the open-world covering
     constraint that every instance of the abstract class must also be an instance of one of its
-    direct subclasses."""
+    direct subclasses.
+
+    .. note:: A warning is emitted when an abstract class has no children (no axiom generated)
+       or only one child (covering axiom degenerates to equivalence Parent ≡ Child).
+       Use this flag to suppress covering axioms entirely if equivalence is undesired."""
 
     def as_graph(self) -> Graph:
         """
@@ -471,6 +475,26 @@ def condition_to_bnode(expr: AnonymousClassExpression) -> BNode | None:
         # must be an instance of at least one of its direct subclasses.
         if cls.abstract and not self.skip_abstract_class_as_unionof_subclasses:
             children = sorted(sv.class_children(cls.name, imports=self.mergeimports, mixins=False, is_a=True))
+            if not children:
+                logger.warning(
+                    "Abstract class '%s' has no children. No covering axiom will be generated.",
+                    cls.name,
+                )
+            elif len(children) == 1:
+                # Warn: with one child C, the covering axiom degenerates to
+                # Parent ⊑ C which, combined with C ⊑ Parent (from is_a),
+                # creates Parent ≡ C (equivalence).  This is semantically
+                # correct per OWL 2 but may be surprising for extensible
+                # ontologies where more children are added later.
+                logger.warning(
+                    "Abstract class '%s' has only 1 direct child ('%s'). "
+                    "The covering axiom makes them equivalent (%s ≡ %s). "
+                    "Use --skip-abstract-class-as-unionof-subclasses to suppress.",
+                    cls.name,
+                    children[0],
+                    cls.name,
+                    children[0],
+                )
             if children:
                 child_uris = [self._class_uri(child) for child in children]
                 union_node = self._union_of(child_uris)
@@ -1569,7 +1593,8 @@ def slot_owl_type(self, slot: SlotDefinition) -> URIRef:
     show_default=True,
     help=(
         "If true, suppress rdfs:subClassOf owl:unionOf(subclasses) covering axioms for abstract classes. "
-        "By default such axioms are emitted for every abstract class that has direct is_a children."
+        "By default such axioms are emitted for every abstract class that has direct is_a children. "
+        "Note: warnings are emitted for abstract classes with zero children (no axiom) or one child (equivalence)."
     ),
 )
 @click.version_option(__version__, "-V", "--version")
diff --git a/tests/linkml/test_generators/test_owlgen.py b/tests/linkml/test_generators/test_owlgen.py
index 062864721..95cb6aca3 100644
--- a/tests/linkml/test_generators/test_owlgen.py
+++ b/tests/linkml/test_generators/test_owlgen.py
@@ -460,6 +460,112 @@ def test_abstract_class_without_subclasses_gets_no_union_of_axiom():
     assert _union_members(g, EX.Orphan) is None
 
 
+def test_abstract_class_with_no_children_emits_warning(caplog):
+    """An abstract class with no children emits a warning about missing coverage.
+
+    When an abstract class has zero subclasses, no covering axiom can be
+    generated.  The warning alerts users that the class hierarchy is incomplete.
+
+    See: mgskjaeveland's review on linkml/linkml#3309.
+    """
+    import logging
+
+    sb = SchemaBuilder()
+    sb.add_class("Orphan", abstract=True)
+    sb.add_defaults()
+
+    with caplog.at_level(logging.WARNING, logger="linkml.generators.owlgen"):
+        g = _owl_graph(sb)
+
+    # No covering axiom emitted
+    assert _union_members(g, EX.Orphan) is None
+
+    # But a warning must be logged
+    assert any("has no children" in msg for msg in caplog.messages), (
+        "Expected a warning about abstract class with no children"
+    )
+    assert any("No covering axiom" in msg for msg in caplog.messages), (
+        "Warning should mention that no covering axiom will be generated"
+    )
+
+
+def test_no_children_warning_suppressed_by_skip_flag(caplog):
+    """When --skip-abstract-class-as-unionof-subclasses is set, no warning for zero children."""
+    import logging
+
+    sb = SchemaBuilder()
+    sb.add_class("Orphan", abstract=True)
+    sb.add_defaults()
+
+    with caplog.at_level(logging.WARNING, logger="linkml.generators.owlgen"):
+        _owl_graph(sb, skip_abstract_class_as_unionof_subclasses=True)
+
+    assert not any("has no children" in msg for msg in caplog.messages)
+
+
+def test_abstract_class_with_single_child_emits_warning(caplog):
+    """An abstract class with one child still gets a covering axiom but emits a warning.
+
+    Per OWL 2 semantics, the covering axiom with a single child creates an
+    equivalence (Parent ≡ Child).  This is logically correct but may surprise
+    users who plan to extend the ontology later.  The generator should warn
+    and recommend ``--skip-abstract-class-as-unionof-subclasses``.
+
+    See: W3C OWL 2 Primer §4.2 — bidirectional rdfs:subClassOf = equivalence.
+    See: mgskjaeveland's review on linkml/linkml#3309.
+    """
+    import logging
+
+    sb = SchemaBuilder()
+    sb.add_class("GrandParent")
+    sb.add_class("Parent", is_a="GrandParent", abstract=True)
+    sb.add_class("Child", is_a="Parent")
+    sb.add_defaults()
+
+    with caplog.at_level(logging.WARNING, logger="linkml.generators.owlgen"):
+        g = _owl_graph(sb)
+
+    # Covering axiom IS still emitted (single child → equivalence is OWL-correct).
+    # With one child, _union_of returns the child URI directly (no owl:unionOf wrapper),
+    # so the covering axiom materialises as Parent rdfs:subClassOf Child.
+    # Combined with Child rdfs:subClassOf Parent (from is_a), this is the equivalence.
+    assert (EX.Parent, RDFS.subClassOf, EX.Child) in g, (
+        "Covering axiom should produce Parent rdfs:subClassOf Child for single-child case"
+    )
+    assert (EX.Child, RDFS.subClassOf, EX.Parent) in g
+    assert (EX.Parent, RDFS.subClassOf, EX.GrandParent) in g
+
+    # But a warning must be logged
+    assert any("only 1 direct child" in msg for msg in caplog.messages), (
+        "Expected a warning about single-child covering axiom creating equivalence"
+    )
+    assert any("--skip-abstract-class-as-unionof-subclasses" in msg for msg in caplog.messages), (
+        "Warning should recommend the skip flag"
+    )
+
+
+def test_single_child_warning_suppressed_by_skip_flag(caplog):
+    """When --skip-abstract-class-as-unionof-subclasses is set, no warning is emitted.
+
+    The skip flag suppresses covering axioms entirely, so the single-child
+    equivalence case never arises.
+    """
+    import logging
+
+    sb = SchemaBuilder()
+    sb.add_class("Parent", abstract=True)
+    sb.add_class("Child", is_a="Parent")
+    sb.add_defaults()
+
+    with caplog.at_level(logging.WARNING, logger="linkml.generators.owlgen"):
+        g = _owl_graph(sb, skip_abstract_class_as_unionof_subclasses=True)
+
+    # No covering axiom emitted
+    assert (EX.Parent, RDFS.subClassOf, EX.Child) not in g
+    # No warning either
+    assert not any("only 1 direct child" in msg for msg in caplog.messages)
+
+
 @pytest.mark.parametrize("skip", [False, True])
 def test_union_of_axiom_only_covers_direct_children(skip: bool):
     """Union-of axiom lists only direct is_a children, not grandchildren.