diff --git a/pandas/tools/merge.py b/pandas/tools/merge.py
index de4c7ca42cdb1..b54a84f2b9687 100644
--- a/pandas/tools/merge.py
+++ b/pandas/tools/merge.py
@@ -77,7 +77,7 @@ def get_result(self):
         join_index, left_indexer, right_indexer = self._get_join_info()
 
         # this is a bit kludgy
-        ldata, rdata = self._get_merge_data(self.join_names)
+        ldata, rdata = self._get_merge_data()
 
         # TODO: more efficiently handle group keys to avoid extra consolidation!
         join_op = _BlockJoinOperation([ldata, rdata], join_index,
@@ -154,13 +154,19 @@ def _get_join_info(self):
 
         return join_index, left_indexer, right_indexer
 
-    def _get_merge_data(self, join_names):
+    def _get_merge_data(self):
         """
         Handles overlapping column names etc.
         """
         ldata, rdata = self.left._data, self.right._data
         lsuf, rsuf = self.suffixes
-        exclude_names = [x for x in join_names if x is not None]
+        exclude_names = set(x for x in self.join_names if x is not None)
+        if self.left_on is not None:
+            exclude_names -= set(c.name if hasattr(c, 'name') else c
+                                 for c in self.left_on)
+        if self.right_on is not None:
+            exclude_names -= set(c.name if hasattr(c, 'name') else c
+                                 for c in self.right_on)
         ldata, rdata = ldata._maybe_rename_join(rdata, lsuf, rsuf,
                                                 exclude=exclude_names,
                                                 copydata=False)
diff --git a/pandas/tools/tests/test_merge.py b/pandas/tools/tests/test_merge.py
index 232a18f78c286..eb4b1cc75de72 100644
--- a/pandas/tools/tests/test_merge.py
+++ b/pandas/tools/tests/test_merge.py
@@ -177,6 +177,14 @@ def test_handle_overlap(self):
         self.assert_('key1.foo' in joined)
         self.assert_('key1.bar' in joined)
 
+    def test_handle_overlap_arbitrary_key(self):
+        joined = merge(self.df, self.df2,
+                       left_on='key2', right_on='key1',
+                       suffixes=['.foo', '.bar'])
+
+        self.assert_('key1.foo' in joined)
+        self.assert_('key2.bar' in joined)
+
     def test_merge_common(self):
         joined = merge(self.df, self.df2)
         exp = merge(self.df, self.df2, on=['key1', 'key2'])