diff --git a/cms/djangoapps/contentstore/management/commands/tests/test_import.py b/cms/djangoapps/contentstore/management/commands/tests/test_import.py
index f613c27875..7a56893607 100644
--- a/cms/djangoapps/contentstore/management/commands/tests/test_import.py
+++ b/cms/djangoapps/contentstore/management/commands/tests/test_import.py
@@ -11,6 +11,7 @@ from django.core.management import call_command
 
 from django_comment_common.utils import are_permissions_roles_seeded
 from xmodule.modulestore.django import modulestore
+from xmodule.modulestore import ModuleStoreEnum
 from xmodule.modulestore.tests.django_utils import ModuleStoreTestCase
 
 
@@ -27,7 +28,7 @@ class TestImport(ModuleStoreTestCase):
                     'course="{0.course}"/>'.format(course_id))
 
         with open(os.path.join(directory, "course", "{0.run}.xml".format(course_id)), "w+") as f:
-            f.write('<course></course>')
+            f.write('<course><chapter name="Test Chapter"></chapter></course>')
 
         return directory
 
@@ -72,3 +73,23 @@ class TestImport(ModuleStoreTestCase):
         # Now load up the course with a similar course_id and verify it loads
         call_command('import', self.content_dir, self.course_dir)
         self.assertIsNotNone(store.get_course(self.truncated_key))
+
+    def test_existing_course_with_different_modulestore(self):
+        """
+        Checks that a course that originally existed in old mongo can be re-imported when
+        split is the default modulestore.
+        """
+        with modulestore().default_store(ModuleStoreEnum.Type.mongo):
+            call_command('import', self.content_dir, self.good_dir)
+
+        # Clear out the modulestore mappings, else when the next import command goes to create a destination
+        # course_key, it will find the existing course and return the mongo course_key. To reproduce TNL-1362,
+        # the destination course_key needs to be the one for split modulestore.
+        modulestore().mappings = {}
+
+        with modulestore().default_store(ModuleStoreEnum.Type.split):
+            call_command('import', self.content_dir, self.good_dir)
+            course = modulestore().get_course(self.base_course_key)
+            # With the bug, this fails because the chapter's course_key is the split mongo form,
+            # while the course's course_key is the old mongo form.
+            self.assertEqual(unicode(course.location.course_key), unicode(course.children[0].course_key))
diff --git a/common/lib/xmodule/xmodule/modulestore/xml_importer.py b/common/lib/xmodule/xmodule/modulestore/xml_importer.py
index e697c61011..1054520a7e 100644
--- a/common/lib/xmodule/xmodule/modulestore/xml_importer.py
+++ b/common/lib/xmodule/xmodule/modulestore/xml_importer.py
@@ -195,11 +195,18 @@ def import_from_xml(
         if target_course_id is not None:
             dest_course_id = target_course_id
         else:
+            # Note that dest_course_id will be in the format for the default modulestore.
             dest_course_id = store.make_course_key(course_key.org, course_key.course, course_key.run)
 
+        existing_course_id = store.has_course(dest_course_id, ignore_case=True)
+        # store.has_course will return the course_key in the format for the modulestore in which it was found.
+        # This may be different from dest_course_id, so correct to the format found.
+        if existing_course_id:
+            dest_course_id = existing_course_id
+
         runtime = None
         # Creates a new course if it doesn't already exist
-        if create_course_if_not_present and not store.has_course(dest_course_id, ignore_case=True):
+        if create_course_if_not_present and not existing_course_id:
             try:
                 new_course = store.create_course(dest_course_id.org, dest_course_id.course, dest_course_id.run, user_id)
                 runtime = new_course.runtime