diff --git a/biology/iqtree/Makefile b/biology/iqtree/Makefile
index 6d4837298edc..af11d67a7c5a 100644
--- a/biology/iqtree/Makefile
+++ b/biology/iqtree/Makefile
@@ -1,40 +1,39 @@
 PORTNAME=	iqtree
 DISTVERSIONPREFIX=	v
-DISTVERSION=	2.4.0
-PORTREVISION=	3
+DISTVERSION=	3.0.1
 CATEGORIES=	biology
 
 MAINTAINER=	jrm@FreeBSD.org
 COMMENT=	Efficient phylogenomic software by maximum likelihood
 WWW=		http://www.iqtree.org/
 
 LICENSE=	GPLv2
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 BROKEN_aarch64=	fails to compile: unrecognized command line option '-msse3'
 BROKEN_powerpc64=	fails to build: GCC version must be at least 4.8!
 NOT_FOR_ARCHS=	armv6 armv7 i386 powerpc
 NOT_FOR_ARCHS_REASON=	32-bit compilation is not supported
 
 LIB_DEPENDS=	libboost_filesystem.so:devel/boost-libs
 
 USES=		cmake eigen:3
 USE_GITHUB=	yes
-GH_PROJECT=	iqtree2
+GH_PROJECT=	iqtree3
 GH_TUPLE=	tothuhien:lsd2:c61110f3a4fa05325b45c97b2134792ff9d55d4c:tothuhien/lsd2 \
-		iqtree:cmaple:3946f47731699573ed2268e00aa7996a3458d4eb:iqtree/cmaple
+		iqtree:cmaple:29df93e77b7ad159b19e8cdd8150545baa1221ae:iqtree/cmaple
 
 PLIST_FILES=	bin/iqtree
 PORTEXAMPLES=	custom_distributions.txt example.cf example.nex example.phy \
 		models.nex tree.nwk
 
 OPTIONS_DEFINE=	EXAMPLES
 
 do-install:
-	${INSTALL_PROGRAM} ${BUILD_WRKSRC}/iqtree2 ${STAGEDIR}${PREFIX}/bin/iqtree
+	${INSTALL_PROGRAM} ${BUILD_WRKSRC}/iqtree3 ${STAGEDIR}${PREFIX}/bin/iqtree
 
 do-install-EXAMPLES-on:
 	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
 	${INSTALL_DATA} ${WRKSRC}/example/* ${STAGEDIR}${EXAMPLESDIR}
 
 .include <bsd.port.mk>
diff --git a/biology/iqtree/distinfo b/biology/iqtree/distinfo
index ae72ac55ee39..f42a38d7c5f0 100644
--- a/biology/iqtree/distinfo
+++ b/biology/iqtree/distinfo
@@ -1,7 +1,7 @@
-TIMESTAMP = 1739123157
-SHA256 (iqtree-iqtree2-v2.4.0_GH0.tar.gz) = 06a3351de0ed3c44a3e197e94a5d0cc3de7359c0be79eab1f41fb83459234619
-SIZE (iqtree-iqtree2-v2.4.0_GH0.tar.gz) = 5524827
+TIMESTAMP = 1765767206
+SHA256 (iqtree-iqtree3-v3.0.1_GH0.tar.gz) = 2daff8eaa24faaeac3dee9ac63af9fd7b79cc94cf7031671f0068b051b12c55f
+SIZE (iqtree-iqtree3-v3.0.1_GH0.tar.gz) = 5172154
 SHA256 (tothuhien-lsd2-c61110f3a4fa05325b45c97b2134792ff9d55d4c_GH0.tar.gz) = 9bbeaa0f8f35783c1d8dec74df6c93a804dbca808fa04484f9123de4e7258b53
 SIZE (tothuhien-lsd2-c61110f3a4fa05325b45c97b2134792ff9d55d4c_GH0.tar.gz) = 1529381
-SHA256 (iqtree-cmaple-3946f47731699573ed2268e00aa7996a3458d4eb_GH0.tar.gz) = 712016835e40c26c1e69529fca1bec46a7102ede3775e1b4b6589c4b6074410a
-SIZE (iqtree-cmaple-3946f47731699573ed2268e00aa7996a3458d4eb_GH0.tar.gz) = 4806755
+SHA256 (iqtree-cmaple-29df93e77b7ad159b19e8cdd8150545baa1221ae_GH0.tar.gz) = f8b5115823614b4c710a13ded1b38b59953c9f3127ced46246d1a4b1db026e37
+SIZE (iqtree-cmaple-29df93e77b7ad159b19e8cdd8150545baa1221ae_GH0.tar.gz) = 4807064