diff --git a/biology/py-scikit-bio/Makefile b/biology/py-scikit-bio/Makefile
index 03e22bd69308..67ae12a909ec 100644
--- a/biology/py-scikit-bio/Makefile
+++ b/biology/py-scikit-bio/Makefile
@@ -1,51 +1,51 @@
 PORTNAME=	scikit-bio
-DISTVERSION=	0.6.0
+DISTVERSION=	0.6.1
 CATEGORIES=	biology education python
 MASTER_SITES=	PYPI
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Data structures, algorithms, educational resources for bioinformatics
 WWW=		http://scikit-bio.org/
 
 LICENSE=	BSD3CLAUSE
 LICENSE_FILE=	${WRKSRC}/LICENSE.txt
 
 BROKEN_aarch64=	fails to build: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size, see https://github.com/biocore/scikit-bio/issues/1816
 
 BUILD_DEPENDS=	${PYNUMPY} \
 		${PY_SETUPTOOLS} \
 		${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR}
 RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}biom-format>0:biology/py-biom-format@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}decorator>=3.4.2:devel/py-decorator@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}h5py>=3.6.0:science/py-h5py@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}hdmedians>=0.14.1:math/py-hdmedians@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}ipython>=3.2.0:devel/ipython@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}matplotlib>=1.4.3:math/py-matplotlib@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}natsort>=4.0.3:devel/py-natsort@${PY_FLAVOR} \
 		${PYNUMPY} \
 		${PYTHON_PKGNAMEPREFIX}pandas>=1.5.0:math/py-pandas@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}requests>=2.20.0:www/py-requests@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}scikit-learn>=0.19.1:science/py-scikit-learn@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}scipy>=1.9.0:science/py-scipy@${PY_FLAVOR}
 
 USES=		python
 USE_PYTHON=	pep517 cython autoplist pytest # tests fail to run, see https://github.com/biocore/scikit-bio/issues/1846
 
 TEST_ENV=	${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}
 
 CONFLICTS_INSTALL=	${PYTHON_PKGNAMEPREFIX}ddtrace # lib/python3.8/site-packages/benchmarks/__init__.py
 
 .include <bsd.port.options.mk>
 
 .if ${ARCH} == i386
 CFLAGS+=	-msse2 # workaround for https://github.com/biocore/scikit-bio/issues/1727
 CXXFLAGS+=	-msse2
 .endif
 
 post-install:
 	@${STRIP_CMD} \
 		${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/skbio/*/*${PYTHON_EXT_SUFFIX}.so \
 		${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/skbio/*/*/*${PYTHON_EXT_SUFFIX}.so
 
 .include <bsd.port.mk>
diff --git a/biology/py-scikit-bio/distinfo b/biology/py-scikit-bio/distinfo
index 558a18b5c5f1..97c19baf5398 100644
--- a/biology/py-scikit-bio/distinfo
+++ b/biology/py-scikit-bio/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1712349674
-SHA256 (scikit-bio-0.6.0.tar.gz) = 10105a7c3c15ae5910244927f29ba7aa35234b19ebe6513b8484547343b2c10f
-SIZE (scikit-bio-0.6.0.tar.gz) = 1739407
+TIMESTAMP = 1718789862
+SHA256 (scikit-bio-0.6.1.tar.gz) = 2f62d90fb44990d90593f2312398989c816081868c4cc6aedba170893f397b8c
+SIZE (scikit-bio-0.6.1.tar.gz) = 2683273
diff --git a/biology/py-scikit-bio/files/patch-pyproject.toml b/biology/py-scikit-bio/files/patch-pyproject.toml
deleted file mode 100644
index 67286b671d40..000000000000
--- a/biology/py-scikit-bio/files/patch-pyproject.toml
+++ /dev/null
@@ -1,10 +0,0 @@
---- pyproject.toml.orig	2023-08-03 04:59:44 UTC
-+++ pyproject.toml
-@@ -1,6 +1,6 @@
- [build-system]
- # https://numpy.org/doc/stable/dev/depending_on_numpy.html#adding-a-dependency-on-numpy
--requires = ["Cython>=0.29.32", "oldest-supported-numpy", "setuptools", "wheel"]
-+requires = ["Cython>=0.29.32", "numpy", "setuptools", "wheel"]
- 
- [tool.pytest.ini_options]
- filterwarnings = [