diff --git a/setup.cfg b/setup.cfg
index 19b5ade62..412bab3f6 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -3,6 +3,7 @@
 # file, you can obtain one at http://mozilla.org/MPL/2.0/.
 
 [pep8]
+filename = *.py,*.pyx
 exclude = .git,__pycache__,.vagrant,bin/peep.py,build,node_modules
 # E121,E123,E126,E226,E24,E704: Ignored in default pep8 config:
 # https://github.com/jcrocholl/pep8/blob/8ca030e2d8f6d377631bae69a18307fb2d051049/pep8.py#L68
@@ -15,6 +16,7 @@ max-line-length = 140
 # flake8 is a combination of pyflakes & pep8.
 # Unfortunately we have to mostly duplicate the above, since some tools use
 # pep8's config (eg autopep8) so we can't just define everything under [flake8].
+filename = *.py,*.pyx
 exclude = .git,__pycache__,.vagrant,bin/peep.py,build,node_modules
 # The ignore list for pep8 above, plus our own PyFlakes addition:
 # F403: 'from module import *' used; unable to detect undefined names