diff --git a/biology/py-pyrodigal/Makefile b/biology/py-pyrodigal/Makefile
index 7d135a8b0e3a..4dd1a482af38 100644
--- a/biology/py-pyrodigal/Makefile
+++ b/biology/py-pyrodigal/Makefile
@@ -1,31 +1,31 @@
 PORTNAME=	pyrodigal
-DISTVERSION=	3.4.1
+DISTVERSION=	3.5.0
 CATEGORIES=	biology python
 MASTER_SITES=	PYPI
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Python binding for Prodigal, an ORF finder for genomes and metagenomes
 WWW=		https://github.com/althonos/pyrodigal/
 
 LICENSE=	GPLv3
 LICENSE_FILE=	${WRKSRC}/COPYING
 
 BUILD_DEPENDS=	${PYTHON_PKGNAMEPREFIX}cython3>0:lang/cython3@${PY_FLAVOR}
 TEST_DEPENDS=	${PYTHON_PKGNAMEPREFIX}archspec>0:devel/py-archspec@${PY_FLAVOR}
 
 USES=		python
 USE_PYTHON=	distutils concurrent autoplist pytest # cython: cython3 isn't yet supported by python.mk
 
 TEST_ENV=	${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}
 
 post-build:
 	@cd ${BUILD_WRKSRC} && ${SETENV} ${MAKE_ENV} ${PYTHON_CMD} setup.py build_ext --inplace
 
 post-install:
 	@${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/pyrodigal/lib${PYTHON_EXT_SUFFIX}.so
 
 do-test:
 	@cd ${TEST_WRKSRC} && ${SETENV} ${TEST_ENV} ${PYTHON_CMD} -m unittest discover -vv
 
 .include <bsd.port.mk>
diff --git a/biology/py-pyrodigal/distinfo b/biology/py-pyrodigal/distinfo
index ce200fb3c956..673151f16f32 100644
--- a/biology/py-pyrodigal/distinfo
+++ b/biology/py-pyrodigal/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1716658828
-SHA256 (pyrodigal-3.4.1.tar.gz) = 65963ad8cf651f408758e7fa74cbf793eae9720310f0ef8781ee1a285d435326
-SIZE (pyrodigal-3.4.1.tar.gz) = 2577599
+TIMESTAMP = 1721281827
+SHA256 (pyrodigal-3.5.0.tar.gz) = f80bf17a2388e4007c65312c7ed84b661e0244be1ef8ef74006f4967a3591d09
+SIZE (pyrodigal-3.5.0.tar.gz) = 2578346