diff --git a/biology/checkm/Makefile b/biology/checkm/Makefile
index 7994bb0f8748..cb7cc7108d4a 100644
--- a/biology/checkm/Makefile
+++ b/biology/checkm/Makefile
@@ -11,6 +11,9 @@ WWW=		https://ecogenomics.github.io/CheckM/
 LICENSE=	GPLv3
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
+DEPRECATED=	Depends on expired science/py-DendroPy
+EXPIRATION_DATE=2025-06-01
+
 RUN_DEPENDS=	${PYNUMPY} \
 		${PYTHON_PKGNAMEPREFIX}DendroPy>0:science/py-DendroPy@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \