diff --git a/biology/bedtools/Makefile b/biology/bedtools/Makefile
index a69f31ec0bbb..7e8b367384c3 100644
--- a/biology/bedtools/Makefile
+++ b/biology/bedtools/Makefile
@@ -1,30 +1,30 @@
 PORTNAME=		bedtools
 DISTVERSIONPREFIX=	v
-DISTVERSION=		2.30.0
+DISTVERSION=		2.31.0
 CATEGORIES=		biology
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Toolset for genome set arithmetic such as intersect, union
 WWW=		https://bedtools.readthedocs.org/
 
 LICENSE=	MIT
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 TEST_DEPENDS=	bash:shells/bash
 
 USES=		compiler:c++11-lang gmake python
 USE_GITHUB=	yes
 
 GH_ACCOUNT=	arq5x
 GH_PROJECT=	bedtools2
 
 pre-configure:
 	@${REINPLACE_CMD} -e 's|python|${PYTHON_CMD}|g' ${WRKSRC}/Makefile
 
 post-install:
 	${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/bedtools
 
 do-test:
 	(cd ${WRKSRC}/test && bash test.sh)
 
 .include <bsd.port.mk>
diff --git a/biology/bedtools/distinfo b/biology/bedtools/distinfo
index 7a106b0489f7..ad0fff26a477 100644
--- a/biology/bedtools/distinfo
+++ b/biology/bedtools/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1611493289
-SHA256 (arq5x-bedtools2-v2.30.0_GH0.tar.gz) = c575861ec746322961cd15d8c0b532bb2a19333f1cf167bbff73230a7d67302f
-SIZE (arq5x-bedtools2-v2.30.0_GH0.tar.gz) = 20639858
+TIMESTAMP = 1682717508
+SHA256 (arq5x-bedtools2-v2.31.0_GH0.tar.gz) = 183cf9a96aabc50ef4bd557a53fd01557a123c05a0dc87651371878f357439ec
+SIZE (arq5x-bedtools2-v2.31.0_GH0.tar.gz) = 21085982