diff --git a/srcpkgs/nauty/patches/dont-test-clz-if-disabled.patch b/srcpkgs/nauty/patches/dont-test-clz-if-disabled.patch
new file mode 100644
index 00000000000..d8e749db1bf
--- /dev/null
+++ b/srcpkgs/nauty/patches/dont-test-clz-if-disabled.patch
@@ -0,0 +1,15 @@
+--- a/configure.ac
++++ b/configure.ac
+@@ -453,11 +453,11 @@
+ echo CFLAGS="$CFLAGS"
+ echo MORECFLAGS="$MORECFLAGS"
+ 
++AS_IF([test "$allow_clz" -eq 1],
+ dnl --check if lzcnt instruction is available and requested
+ AC_MSG_CHECKING(if lzcnt instruction is available and requested)
+ AC_RUN_IFELSE([AC_LANG_PROGRAM([],[[if (__builtin_cpu_supports("bmi")) return 0; else return 1;]])],
+   lzsup=1,lzsup=0)
+-AS_IF([test "$allow_clz" -eq 1],
+       [have_hwlzcnt=$lzsup
+ test -f /proc/cpuinfo && $EGREP -i "abm|bmi1" /proc/cpuinfo >/dev/null && have_hwlzcnt=1 
+ test $have_hwlzcnt -eq 0 && sysctl machdep.cpu.features 2>/dev/null | $EGREP -i "bmi1|abm" >/dev/null && have_hwlzcnt=1
diff --git a/srcpkgs/nauty/patches/fix-runalltests.patch b/srcpkgs/nauty/patches/fix-runalltests.patch
deleted file mode 100644
index 34e1692cf6e..00000000000
--- a/srcpkgs/nauty/patches/fix-runalltests.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/runalltests.in	2024-08-26 00:55:55.000000000 -0300
-+++ b/runalltests.in	2024-09-08 09:30:04.032719770 -0300
-@@ -121,7 +121,7 @@
- runonetest "./geng -q -TD6 10 | ./ransubg -qS765 -P9/10 | ./countg --NN,A,G,GG" "" nautestv.ans
- runonetest "./genrang -q -P3 -S1234 70 1000 | ./countg --G,GG" "" nautestw.ans
- runonetest "./genrang -q -P4 -z -S1234 70 500 | ./countg --G,GG" "" nautestx.ans
--runonetest "./geng -q -bT 12 | ./ranlabg -qS7654 -m5 | uniqg -u" "" nautesty.ans
-+runonetest "./geng -q -bT 12 | ./ranlabg -qS7654 -m5 | ./uniqg -u" "" nautesty.ans
- 
- echo " "
- 
diff --git a/srcpkgs/nauty/template b/srcpkgs/nauty/template
index aea4e4a6eb0..4c1009a8c34 100644
--- a/srcpkgs/nauty/template
+++ b/srcpkgs/nauty/template
@@ -1,6 +1,6 @@
 # Template file for 'nauty'
 pkgname=nauty
-version=2.8.9
+version=2.9.0
 revision=1
 build_style=gnu-configure
 make_install_args="includedir=/usr/include/nauty
@@ -10,14 +10,14 @@ short_desc="Compute the automorphism groups of graphs and digraphs"
 maintainer="Gonzalo Tornaría <tornaria@cmat.edu.uy>"
 license="Apache-2.0"
 homepage="https://pallini.di.uniroma1.it/"
-changelog="https://pallini.di.uniroma1.it/changes24-28.txt"
-distfiles="https://pallini.di.uniroma1.it/nauty${version//./_}.tar.gz"
-checksum=c97ab42bf48796a86a598bce3e9269047ca2b32c14fc23e07208a244fe52c4ee
+changelog="https://pallini.di.uniroma1.it/changes24-29.txt"
+distfiles="https://github.com/lonnen/nauty/archive/refs/tags/nauty${version//./_}.tar.gz"
+checksum=d9c76d55cbb36b0abf05e7b39b20f6966f419fcc78225435558bed91376fe004
 
 build_options="native_build"
 
 if [ -z "$build_option_native_build" ]; then
-	configure_args="--enable-generic --disable-popcnt"
+	configure_args="--enable-generic --disable-popcnt --disable-clz"
 fi
 
 pre_configure() {