diff --git a/biology/bedtools/Makefile b/biology/bedtools/Makefile
index 7e8b367384c3..4f0b519d87f5 100644
--- a/biology/bedtools/Makefile
+++ b/biology/bedtools/Makefile
@@ -1,30 +1,30 @@
 PORTNAME=		bedtools
 DISTVERSIONPREFIX=	v
-DISTVERSION=		2.31.0
+DISTVERSION=		2.31.1
 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 ad0fff26a477..eb599d15d598 100644
--- a/biology/bedtools/distinfo
+++ b/biology/bedtools/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1682717508
-SHA256 (arq5x-bedtools2-v2.31.0_GH0.tar.gz) = 183cf9a96aabc50ef4bd557a53fd01557a123c05a0dc87651371878f357439ec
-SIZE (arq5x-bedtools2-v2.31.0_GH0.tar.gz) = 21085982
+TIMESTAMP = 1699454464
+SHA256 (arq5x-bedtools2-v2.31.1_GH0.tar.gz) = 79a1ba318d309f4e74bfa74258b73ef578dccb1045e270998d7fe9da9f43a50e
+SIZE (arq5x-bedtools2-v2.31.1_GH0.tar.gz) = 21085970