diff --git a/sys-cluster/charliecloud/charliecloud-0.43.ebuild b/sys-cluster/charliecloud/charliecloud-0.43.ebuild
index 892f0ea7952ce..52cfc8762d36b 100644
--- a/sys-cluster/charliecloud/charliecloud-0.43.ebuild
+++ b/sys-cluster/charliecloud/charliecloud-0.43.ebuild
@@ -32,6 +32,10 @@ DOCS=( NOTICE README.rst )
 
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
+# Configure check, only recent (not yet released) dev-libs/boehm-gc carry this function
+# in non-threaded mode, see #968001.
+QA_CONFIG_IMPL_DECL_SKIP=( GC_set_markers_count )
+
 DEPEND="elibc_musl? ( sys-libs/argp-standalone )"
 COMMON_DEPEND="
 	ch-image? (
diff --git a/sys-cluster/charliecloud/charliecloud-9999.ebuild b/sys-cluster/charliecloud/charliecloud-9999.ebuild
index 892f0ea7952ce..52cfc8762d36b 100644
--- a/sys-cluster/charliecloud/charliecloud-9999.ebuild
+++ b/sys-cluster/charliecloud/charliecloud-9999.ebuild
@@ -32,6 +32,10 @@ DOCS=( NOTICE README.rst )
 
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
+# Configure check, only recent (not yet released) dev-libs/boehm-gc carry this function
+# in non-threaded mode, see #968001.
+QA_CONFIG_IMPL_DECL_SKIP=( GC_set_markers_count )
+
 DEPEND="elibc_musl? ( sys-libs/argp-standalone )"
 COMMON_DEPEND="
 	ch-image? (