diff --git a/math/py-pynndescent/Makefile b/math/py-pynndescent/Makefile
index 42e7da1bd46a..044909079c95 100644
--- a/math/py-pynndescent/Makefile
+++ b/math/py-pynndescent/Makefile
@@ -1,26 +1,26 @@
 PORTNAME=	pynndescent
-DISTVERSION=	0.5.8
+DISTVERSION=	0.5.9
 CATEGORIES=	math python
 MASTER_SITES=	PYPI
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Python nearest neighbor descent for approximate nearest neighbors
 WWW=		https://github.com/lmcinnes/pynndescent
 
 LICENSE=	APACHE20
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 RUN_DEPENDS=	${PYNUMPY} \
-		${PYTHON_PKGNAMEPREFIX}joblib>0:devel/py-joblib@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}llvmlite>=0.34:devel/py-llvmlite@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}joblib>0.11:devel/py-joblib@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}llvmlite>=0.30:devel/py-llvmlite@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}numba>=0.51.2:devel/py-numba@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}scikit-learn>=0.18:science/py-scikit-learn@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}scipy>=1.0:science/py-scipy@${PY_FLAVOR}
 
-USES=		python:3.5+
-USE_PYTHON=	distutils autoplist pytest
+USES=		python:3.6+
+USE_PYTHON=	distutils autoplist pytest # tests fail to run, see https://github.com/lmcinnes/pynndescent/issues/216
 
 NO_ARCH=	yes
 
 .include <bsd.port.mk>
diff --git a/math/py-pynndescent/distinfo b/math/py-pynndescent/distinfo
index 07de1845fabd..5a7c30034ead 100644
--- a/math/py-pynndescent/distinfo
+++ b/math/py-pynndescent/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1678612370
-SHA256 (pynndescent-0.5.8.tar.gz) = a7c552569bf604a101fd54bba1d27c12389e065945dee3a6777a518c63a46f2b
-SIZE (pynndescent-0.5.8.tar.gz) = 1138925
+TIMESTAMP = 1681884462
+SHA256 (pynndescent-0.5.9.tar.gz) = bacf78d914f44724528adcfea9681ddd6c873d14f4b0526c0ff6b9f243338042
+SIZE (pynndescent-0.5.9.tar.gz) = 1139286