diff --git a/src/matUtils/select.cpp b/src/matUtils/select.cpp
index 10b46a5b..9e217172 100644
--- a/src/matUtils/select.cpp
+++ b/src/matUtils/select.cpp
@@ -360,7 +360,9 @@ std::unordered_map<std::string,std::unordered_map<std::string,std::string>> read
             first = false;
         } else {
             for (size_t i=1; i < words.size(); i++) {
-                metamap[keys[i]][words[0]] = words[i];
+                if (samples_to_use.find(words[0]) != samples_to_use.end()) {
+                    metamap[keys[i]][words[0]] = words[i];
+                }
             }
         }
     }
@@ -529,4 +531,4 @@ std::pair<std::vector<std::string>, size_t> get_closest_samples(MAT::Tree* T, st
         dist_to_orig_parent += parent_branch_length;
     }
     return closest_samples;
-}
\ No newline at end of file
+}