diff --git a/biology/samtools/Makefile b/biology/samtools/Makefile
index f0ce1807eecd..8b38c60021ae 100644
--- a/biology/samtools/Makefile
+++ b/biology/samtools/Makefile
@@ -1,27 +1,29 @@
 PORTNAME=	samtools
-DISTVERSION=	1.22
+DISTVERSION=	1.23.1
 CATEGORIES=	biology
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Tools for manipulating next-generation sequencing data
 WWW=		https://www.htslib.org/
 
 LICENSE=	MIT
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 BUILD_DEPENDS=	htslib>=1.22:biology/htslib
 LIB_DEPENDS=	libhts.so:biology/htslib
 TEST_DEPENDS=	bash:shells/bash
 
 USES=		autoreconf gmake localbase ncurses perl5 python:env shebangfix
 
 USE_GITHUB=	yes
 
 USE_PERL5=	test
 GNU_CONFIGURE=	yes
 GNU_CONFIGURE_MANPREFIX=	${PREFIX}/share
 SHEBANG_FILES=	misc/*.pl misc/plot-bamstats test/test.pl
 
+CONFIGURE_ARGS=	--with-htslib=system
+
 TEST_TARGET=	test
 
 .include <bsd.port.mk>
diff --git a/biology/samtools/distinfo b/biology/samtools/distinfo
index 69760896c894..2b86f5f2668a 100644
--- a/biology/samtools/distinfo
+++ b/biology/samtools/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1748951307
-SHA256 (samtools-samtools-1.22_GH0.tar.gz) = dbe62a97d19634a930033ce302b340a5109263efc371b83481182385a98bcdda
-SIZE (samtools-samtools-1.22_GH0.tar.gz) = 5742299
+TIMESTAMP = 1774784873
+SHA256 (samtools-samtools-1.23.1_GH0.tar.gz) = 61314c16f6b502998f79c8d5d3d92f0ab1aab1ca23d60b8abae74e53a4119c87
+SIZE (samtools-samtools-1.23.1_GH0.tar.gz) = 5758667