diff --git a/ipyrad/assemble/util.py b/ipyrad/assemble/util.py
index <HASH>..<HASH> 100644
--- a/ipyrad/assemble/util.py
+++ b/ipyrad/assemble/util.py
@@ -244,6 +244,10 @@ def merge_pairs(data, files_to_merge, merged_file, merge):
             raise IPyradWarningExit("    Attempting to merge file that "\
                                         "doesn't exist - {}.".format(f))
 
+    ## If it already exists, clean up the old merged file
+    if os.path.exists(merged_file):
+        os.remove(merged_file)
+
     ## if merge then catch nonmerged in a separate file
     if merge:
         nonmerged1 = tempfile.NamedTemporaryFile(mode='wb',
Fixed a nasty bug in merge_pairs that resulted in constant reconcatenation to the merged outfile