diff --git a/gtsam/config.h.in b/gtsam/config.h.in
index 9d1bd4ebd..9f7106187 100644
--- a/gtsam/config.h.in
+++ b/gtsam/config.h.in
@@ -77,3 +77,6 @@
 
 // Support Metis-based nested dissection
 #cmakedefine GTSAM_TANGENT_PREINTEGRATION
+
+// Whether to use the system installed Metis instead of the provided one
+#cmakedefine GTSAM_USE_SYSTEM_METIS
diff --git a/gtsam_unstable/partition/FindSeparator-inl.h b/gtsam_unstable/partition/FindSeparator-inl.h
index ce657e7a0..2e48b0d45 100644
--- a/gtsam_unstable/partition/FindSeparator-inl.h
+++ b/gtsam_unstable/partition/FindSeparator-inl.h
@@ -20,6 +20,8 @@
 
 #include "FindSeparator.h"
 
+#ifndef GTSAM_USE_SYSTEM_METIS
+
 extern "C" {
 #include <metis.h>
 #include "metislib.h"
@@ -564,3 +566,5 @@ namespace gtsam { namespace partition {
   }
 
 }} //namespace
+
+#endif
diff --git a/gtsam_unstable/partition/tests/testFindSeparator.cpp b/gtsam_unstable/partition/tests/testFindSeparator.cpp
index fe49de928..63acc8f18 100644
--- a/gtsam_unstable/partition/tests/testFindSeparator.cpp
+++ b/gtsam_unstable/partition/tests/testFindSeparator.cpp
@@ -20,6 +20,8 @@ using namespace std;
 using namespace gtsam;
 using namespace gtsam::partition;
 
+#ifndef GTSAM_USE_SYSTEM_METIS
+
 /* ************************************************************************* */
 // x0 - x1 - x2
 // l3        l4
@@ -227,6 +229,8 @@ TEST ( Partition, findSeparator3_with_reduced_camera )
   LONGS_EQUAL(2, partitionTable[28]);
 }
 
+#endif
+
 /* ************************************************************************* */
 int main() { TestResult tr; return TestRegistry::runAllTests(tr);}
 /* ************************************************************************* */