diff --git a/mongoengine/fields.py b/mongoengine/fields.py
index 51a88bdb..d5336117 100644
--- a/mongoengine/fields.py
+++ b/mongoengine/fields.py
@@ -1261,7 +1261,7 @@ class GenericReferenceField(BaseField):
         if document is None:
             return None
 
-        if isinstance(document, (dict, SON)):
+        if isinstance(document, (dict, SON, ObjectId, DBRef)):
             return document
 
         id_field_name = document.__class__._meta['id_field']
diff --git a/mongoengine/queryset/transform.py b/mongoengine/queryset/transform.py
index 4e5553c9..af59917c 100644
--- a/mongoengine/queryset/transform.py
+++ b/mongoengine/queryset/transform.py
@@ -1,6 +1,7 @@
 from collections import defaultdict
 
-from bson import SON
+from bson import ObjectId, SON
+from bson.dbref import DBRef
 import pymongo
 import six
 
@@ -27,6 +28,7 @@ MATCH_OPERATORS = (COMPARISON_OPERATORS + GEO_OPERATORS +
                    STRING_OPERATORS + CUSTOM_OPERATORS)
 
 
+# TODO make this less complex
 def query(_doc_cls=None, **kwargs):
     """Transform a query from Django-style format to Mongo format."""
     mongo_query = {}
@@ -62,6 +64,7 @@ def query(_doc_cls=None, **kwargs):
             parts = []
 
             CachedReferenceField = _import_class('CachedReferenceField')
+            GenericReferenceField = _import_class('GenericReferenceField')
 
             cleaned_fields = []
             for field in fields:
@@ -101,6 +104,16 @@ def query(_doc_cls=None, **kwargs):
                 # 'in', 'nin' and 'all' require a list of values
                 value = [field.prepare_query_value(op, v) for v in value]
 
+            # If we're querying a GenericReferenceField, we need to alter the
+            # key depending on the value:
+            # * If the value is a DBRef, the key should be "field_name._ref".
+            # * If the value is an ObjectId, the key should be "field_name._ref.$id".
+            if isinstance(field, GenericReferenceField):
+                if isinstance(value, DBRef):
+                    parts[-1] += '._ref'
+                elif isinstance(value, ObjectId):
+                    parts[-1] += '._ref.$id'
+
         # if op and op not in COMPARISON_OPERATORS:
         if op:
             if op in GEO_OPERATORS:
@@ -128,11 +141,13 @@ def query(_doc_cls=None, **kwargs):
 
         for i, part in indices:
             parts.insert(i, part)
+
         key = '.'.join(parts)
+
         if op is None or key not in mongo_query:
             mongo_query[key] = value
         elif key in mongo_query:
-            if key in mongo_query and isinstance(mongo_query[key], dict):
+            if isinstance(mongo_query[key], dict):
                 mongo_query[key].update(value)
                 # $max/minDistance needs to come last - convert to SON
                 value_dict = mongo_query[key]
diff --git a/setup.cfg b/setup.cfg
index ac98a0f3..f883b26c 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -8,6 +8,5 @@ tests = tests
 
 [flake8]
 ignore=E501,F401,F403,F405,I201
-exclude=build,dist,docs,venv,venv26,venv3,.tox,.eggs,tests
-max-complexity=42
-application-import-names=mongoengine,tests
+exclude=build,dist,docs,venv,venv3,.tox,.eggs,tests
+max-complexity=45
diff --git a/tests/fields/fields.py b/tests/fields/fields.py
index a22a2561..87beda70 100644
--- a/tests/fields/fields.py
+++ b/tests/fields/fields.py
@@ -2805,6 +2805,38 @@ class FieldTest(unittest.TestCase):
         Post.drop_collection()
         User.drop_collection()
 
+    def test_generic_reference_filter_by_dbref(self):
+        """Ensure we can search for a specific generic reference by
+        providing its ObjectId.
+        """
+        class Doc(Document):
+            ref = GenericReferenceField()
+
+        Doc.drop_collection()
+
+        doc1 = Doc.objects.create()
+        doc2 = Doc.objects.create(ref=doc1)
+
+        doc = Doc.objects.get(ref=DBRef('doc', doc1.pk))
+        self.assertEqual(doc, doc2)
+
+    def test_generic_reference_filter_by_objectid(self):
+        """Ensure we can search for a specific generic reference by
+        providing its DBRef.
+        """
+        class Doc(Document):
+            ref = GenericReferenceField()
+
+        Doc.drop_collection()
+
+        doc1 = Doc.objects.create()
+        doc2 = Doc.objects.create(ref=doc1)
+
+        self.assertTrue(isinstance(doc1.pk, ObjectId))
+
+        doc = Doc.objects.get(ref=doc1.pk)
+        self.assertEqual(doc, doc2)
+
     def test_binary_fields(self):
         """Ensure that binary fields can be stored and retrieved.
         """