diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-2.68-GCC-13.3.0.eb b/easybuild/easyconfigs/s/Stacks/Stacks-2.68-GCC-12.3.0.eb
index d8ef240f28..417ced6d8a 100644
--- a/easybuild/easyconfigs/s/Stacks/Stacks-2.68-GCC-13.3.0.eb
+++ b/easybuild/easyconfigs/s/Stacks/Stacks-2.68-GCC-12.3.0.eb
@@ -9,7 +9,7 @@ description = """Stacks is a software pipeline for building loci from short-read
  for the purpose of building genetic maps and conducting population genomics and phylogeography.
 """
 
-toolchain = {'name': 'GCC', 'version': '13.3.0'}
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
 
 source_urls = ['https://catchenlab.life.illinois.edu/stacks/source/']
 sources = [SOURCELOWER_TAR_GZ]
@@ -20,12 +20,12 @@ checksums = [
 ]
 
 builddependencies = [
-    ('Autotools', '20231222'),
+    ('Autotools', '20220317'),
 ]
 
 dependencies = [
-    ('zlib', '1.3.1'),
-    ('HTSlib', '1.21'),
+    ('zlib', '1.2.13'),
+    ('HTSlib', '1.18'),
 ]
 
 preconfigopts = 'autoreconf -if && '

diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-2.62-foss-2022a.eb b/easybuild/easyconfigs/s/Stacks/Stacks-2.68-GCC-12.3.0.eb
index 9f30e27f06..417ced6d8a 100644
--- a/easybuild/easyconfigs/s/Stacks/Stacks-2.62-foss-2022a.eb
+++ b/easybuild/easyconfigs/s/Stacks/Stacks-2.68-GCC-12.3.0.eb
@@ -1,7 +1,7 @@
 easyblock = 'ConfigureMake'
 
 name = 'Stacks'
-version = '2.62'
+version = '2.68'
 
 homepage = 'https://catchenlab.life.illinois.edu/stacks/'
 description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on
@@ -9,21 +9,35 @@ description = """Stacks is a software pipeline for building loci from short-read
  for the purpose of building genetic maps and conducting population genomics and phylogeography.
 """
 
-toolchain = {'name': 'foss', 'version': '2022a'}
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
 
 source_urls = ['https://catchenlab.life.illinois.edu/stacks/source/']
 sources = [SOURCELOWER_TAR_GZ]
-checksums = ['eee85054b0bf0043c03d4766dfebc00682301b8ba1372fc49e08ecad98d3d13b']
+patches = ['%(name)s-2.68_use-external-htslib.patch']
+checksums = [
+    {'stacks-2.68.tar.gz': '9dc51ea356d60eb4557b0b2d1a8854aafae492aed87f974e0249cc09aa5e7650'},
+    {'Stacks-2.68_use-external-htslib.patch': '20d77e39719107a47e6e9620490c1210a338e3503e79b4e4122518e8404f976e'},
+]
+
+builddependencies = [
+    ('Autotools', '20220317'),
+]
 
 dependencies = [
-    ('zlib', '1.2.12'),
+    ('zlib', '1.2.13'),
+    ('HTSlib', '1.18'),
 ]
 
+preconfigopts = 'autoreconf -if && '
+configopts = '--with-htslib="$EBROOTHTSLIB"'
+
 sanity_check_paths = {
-    'files': ['bin/clone_filter', 'bin/cstacks', 'bin/gstacks', 'bin/kmer_filter', 'bin/phasedstacks',
-              'bin/populations', 'bin/process_radtags', 'bin/process_shortreads', 'bin/sstacks',
-              'bin/tsv2bam', 'bin/ustacks'],
+    'files': [f'bin/{x}' for x in ['clone_filter', 'cstacks', 'gstacks', 'kmer_filter', 'phasedstacks',
+                                   'populations', 'process_radtags', 'process_shortreads', 'sstacks',
+                                   'tsv2bam', 'ustacks']],
     'dirs': [],
 }
 
+sanity_check_commands = ["ustacks -h 2>&1 | grep -q 'ustacks %(version)s'"]
+
 moduleclass = 'bio'