diff --git a/biology/py-cutadapt/Makefile b/biology/py-cutadapt/Makefile
index d787dcd42a55..c9963c7c1ef4 100644
--- a/biology/py-cutadapt/Makefile
+++ b/biology/py-cutadapt/Makefile
@@ -1,31 +1,30 @@
 PORTNAME=	cutadapt
-DISTVERSION=	5.0
-PORTREVISION=	1
+DISTVERSION=	5.1
 CATEGORIES=	biology python
 MASTER_SITES=	PYPI
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
 MAINTAINER=	jadawin@FreeBSD.org
 COMMENT=	Trim adapters from high-throughput sequencing reads
 WWW=		https://github.com/marcelm/cutadapt/
 
 LICENSE=	MIT
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 BUILD_DEPENDS=	${PYTHON_PKGNAMEPREFIX}setuptools-scm>0:devel/py-setuptools-scm@${PY_FLAVOR}
 RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}xopen>=1.6.0:archivers/py-xopen@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}dnaio>=1.2.0:biology/py-dnaio@${PY_FLAVOR}
 TEST_DEPENDS=	${PYTHON_PKGNAMEPREFIX}pytest>0:devel/py-pytest@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}pytest-timeout>0:devel/py-pytest-timeout@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}pytest-mock>0:devel/py-pytest-mock@${PY_FLAVOR}
 
 USES=		python
 USE_PYTHON=	autoplist concurrent cython distutils
 
 post-install:
 	@${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/cutadapt/*.so
 
 do-test:
 	@cd ${WRKSRC} && ${PYTHON_CMD} -m pytest
 
 .include <bsd.port.mk>
diff --git a/biology/py-cutadapt/distinfo b/biology/py-cutadapt/distinfo
index 1613aa2d6c1a..98c60c1e3018 100644
--- a/biology/py-cutadapt/distinfo
+++ b/biology/py-cutadapt/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1736523245
-SHA256 (cutadapt-5.0.tar.gz) = cd66872b6635c068cf223f72fb0cc93b2454088a3e807a550bb36f717d25ae29
-SIZE (cutadapt-5.0.tar.gz) = 251297
+TIMESTAMP = 1749206212
+SHA256 (cutadapt-5.1.tar.gz) = 6bc76345c0a45f6b680cb1164e48eb1f81815c764ec471284ab6234c6653b937
+SIZE (cutadapt-5.1.tar.gz) = 252843
diff --git a/biology/py-cutadapt/files/patch-pyprojetc.toml b/biology/py-cutadapt/files/patch-pyprojetc.toml
new file mode 100644
index 000000000000..7a3ad00ad87c
--- /dev/null
+++ b/biology/py-cutadapt/files/patch-pyprojetc.toml
@@ -0,0 +1,11 @@
+--- pyproject.toml.orig	2025-06-06 12:32:50.569385000 +0200
++++ pyproject.toml	2025-06-06 12:33:10.984604000 +0200
+@@ -9,7 +9,7 @@
+ ]
+ description = "Adapter trimming and other preprocessing of high-throughput sequencing reads"
+ readme = "README.rst"
+-license = "MIT"
++license = {text = "MIT"}
+ classifiers = [
+     "Development Status :: 5 - Production/Stable",
+     "Environment :: Console",