diff --git a/tools/pip/setup.py b/tools/pip/setup.py
index bf007ea1f5a5..2aff243d3ed7 100644
--- a/tools/pip/setup.py
+++ b/tools/pip/setup.py
@@ -135,14 +135,15 @@ def skip_markdown_comments(md):
     elif variant.startswith('CU92'):
         libraries.append('CUDA-9.2')
 
-if variant != 'NATIVE':
+from mxnet.runtime import Features
+if Features().is_enabled("MKLDNN"):
     libraries.append('MKLDNN')
 
 short_description += ' This version uses {0}.'.format(' and '.join(libraries))
 
 package_data = {'mxnet': [os.path.join('mxnet', os.path.basename(LIB_PATH[0]))],
                 'dmlc_tracker': []}
-if variant != 'NATIVE':
+if Features().is_enabled("MKLDNN"):
     shutil.copytree(os.path.join(CURRENT_DIR, 'mxnet-build/3rdparty/mkldnn/include'),
                     os.path.join(CURRENT_DIR, 'mxnet/include/mkldnn'))
 if platform.system() == 'Linux':