diff --git a/src/common/node_select.c b/src/common/node_select.c
index 41fa7dcfa7ac6c9f4e663f5d4a04563633f96930..b79bd625822ad1de98e1bb9ed606469d857de704 100644
--- a/src/common/node_select.c
+++ b/src/common/node_select.c
@@ -251,6 +251,21 @@ extern int slurm_select_init(bool only_default)
 			      "system use --enable-alps-cray-emulation.");
 		}
 #endif
+
+#ifdef HAVE_NATIVE_CRAY
+		if (strcasecmp(type, "select/cray")) {
+			error("%s is incompatible with a native Cray system.",
+			      type);
+			fatal("Use SelectType=select/cray");
+		}
+#else
+		if (!strcasecmp(type, "select/cray")) {
+			fatal("Requested SelectType=select/cray "
+			      "in slurm.conf, but not running on a native Cray "
+			      "system.  If looking to run on a Cray "
+			      "system natively use --enable-native-cray.");
+		}
+#endif
 	}
 
 	select_context_cnt = 0;