diff --git a/mongoengine/queryset/queryset.py b/mongoengine/queryset/queryset.py
index 5077f895..dc5fab4c 100644
--- a/mongoengine/queryset/queryset.py
+++ b/mongoengine/queryset/queryset.py
@@ -71,7 +71,10 @@ class QuerySet(object):
         # If inheritance is allowed, only return instances and instances of
         # subclasses of the class being used
         if document._meta.get('allow_inheritance') is True:
-            self._initial_query = {"_cls": {"$in": self._document._subclasses}}
+            if len(self._document._subclasses) == 1:
+                self._initial_query = {"_cls": self._document._subclasses[0]}
+            else:
+                self._initial_query = {"_cls": {"$in": self._document._subclasses}}
             self._loaded_fields = QueryFieldList(always_include=['_cls'])
         self._cursor_obj = None
         self._limit = None
diff --git a/tests/queryset/queryset.py b/tests/queryset/queryset.py
index 507408d7..07ddf2d9 100644
--- a/tests/queryset/queryset.py
+++ b/tests/queryset/queryset.py
@@ -3392,6 +3392,34 @@ class QuerySetTest(unittest.TestCase):
         self.assertEqual(B.objects.get(a=a).a, a)
         self.assertEqual(B.objects.get(a=a.id).a, a)
 
+    def test_cls_query_in_subclassed_docs(self):
+
+        class Animal(Document):
+            name = StringField()
+
+            meta = {
+                'allow_inheritance': True
+            }
+
+        class Dog(Animal):
+            pass
+
+        class Cat(Animal):
+            pass
+
+        self.assertEqual(Animal.objects(name='Charlie')._query, {
+            'name': 'Charlie',
+            '_cls': { '$in': ('Animal', 'Animal.Dog', 'Animal.Cat') }
+        })
+        self.assertEqual(Dog.objects(name='Charlie')._query, {
+            'name': 'Charlie',
+            '_cls': 'Animal.Dog'
+        })
+        self.assertEqual(Cat.objects(name='Charlie')._query, {
+            'name': 'Charlie',
+            '_cls': 'Animal.Cat'
+        })
+
 
 if __name__ == '__main__':
     unittest.main()