--- a/debian/control
+++ b/debian/control
@@ -5,7 +5,8 @@
            Kevin Murray <kdmfoss@gmail.com>
 Section: python
 Priority: optional
-Build-Depends: debhelper-compat (= 13),
+Build-Depends: cython3,
+               debhelper-compat (= 13),
                dh-python,
                python3-all-dev,
                python3-setuptools,
--- a/debian/rules
+++ b/debian/rules
@@ -8,10 +8,15 @@
 export PYBUILD_NAME=skbio
 export MPLBACKEND=agg
 DOCPKG=python-$(PYBUILD_NAME)-doc
+export USE_CYTHON=1
 
 %:
 	dh $@ --with python3,sphinxdoc --buildsystem=pybuild
 
+override_dh_auto_configure:
+	rm -f skbio/alignment/_ssw_wrapper.c skbio/diversity/_phylogenetic.c skbio/stats/__subsample.c skbio/metadata/_intersection.c
+	dh_auto_configure
+
 override_dh_auto_build-arch:
 	dh_auto_build
 
@@ -43,6 +48,7 @@
 	find doc -name *.doctree -delete
 	rm -rf .pybuild
 	rm -f scikit_bio.egg-info/PKG-INFO scikit_bio.egg-info/SOURCES.txt scikit_bio.egg-info/dependency_links.txt scikit_bio.egg-info/requires.txt scikit_bio.egg-info/top_level.txt
+	rm -f skbio/alignment/_ssw_wrapper.c skbio/diversity/_phylogenetic.c skbio/stats/__subsample.c skbio/metadata/_intersection.c
 
 
 override_dh_sphinxdoc: