diff --git a/doc/source/whatsnew/v0.18.1.txt b/doc/source/whatsnew/v0.18.1.txt
index dbe446f0a7b4f..6ba8edcca59e8 100644
--- a/doc/source/whatsnew/v0.18.1.txt
+++ b/doc/source/whatsnew/v0.18.1.txt
@@ -47,7 +47,7 @@ API changes
 
 
 
-
+- ``pandas.merge()`` and ``DataFrame.join()`` will show a ``UserWarning`` when merging/joining a single- with a multi-leveled dataframe (:issue:`9455`, :issue:`12219`)
 
 
 
diff --git a/pandas/tests/frame/test_axis_select_reindex.py b/pandas/tests/frame/test_axis_select_reindex.py
index 64be1ef460f51..26a88d601ec4b 100644
--- a/pandas/tests/frame/test_axis_select_reindex.py
+++ b/pandas/tests/frame/test_axis_select_reindex.py
@@ -142,6 +142,31 @@ def test_drop_multiindex_not_lexsorted(self):
 
         tm.assert_frame_equal(result, expected)
 
+    def test_merge_join_different_levels(self):
+        # GH 9455
+
+        # first dataframe
+        df1 = DataFrame(columns=['a', 'b'], data=[[1, 11], [0, 22]])
+
+        # second dataframe
+        columns = MultiIndex.from_tuples([('a', ''), ('c', 'c1')])
+        df2 = DataFrame(columns=columns, data=[[1, 33], [0, 44]])
+
+        # merge
+        columns = ['a', 'b', ('c', 'c1')]
+        expected = DataFrame(columns=columns, data=[[1, 11, 33], [0, 22, 44]])
+        with tm.assert_produces_warning(UserWarning):
+            result = pd.merge(df1, df2, on='a')
+        tm.assert_frame_equal(result, expected)
+
+        # join, see discussion in GH 12219
+        columns = ['a', 'b', ('a', ''), ('c', 'c1')]
+        expected = DataFrame(columns=columns,
+                             data=[[1, 11, 0, 44], [0, 22, 1, 33]])
+        with tm.assert_produces_warning(UserWarning):
+            result = df1.join(df2, on='a')
+        tm.assert_frame_equal(result, expected)
+
     def test_reindex(self):
         newFrame = self.frame.reindex(self.ts1.index)
 
diff --git a/pandas/tools/merge.py b/pandas/tools/merge.py
index 82fdf0a3d3b46..895f5b74a3e80 100644
--- a/pandas/tools/merge.py
+++ b/pandas/tools/merge.py
@@ -2,6 +2,8 @@
 SQL-style merge routines
 """
 
+import warnings
+
 import numpy as np
 from pandas.compat import range, lrange, lzip, zip, map, filter
 import pandas.compat as compat
@@ -193,6 +195,13 @@ def __init__(self, left, right, how='inner', on=None,
                 'can not merge DataFrame with instance of '
                 'type {0}'.format(type(right)))
 
+        # warn user when merging between different levels
+        if left.columns.nlevels != right.columns.nlevels:
+            msg = ('merging between different levels can give an unintended '
+                   'result ({0} levels on the left, {1} on the right)')
+            msg = msg.format(left.columns.nlevels, right.columns.nlevels)
+            warnings.warn(msg, UserWarning)
+
         # note this function has side effects
         (self.left_join_keys,
          self.right_join_keys,
diff --git a/pandas/tools/tests/test_merge.py b/pandas/tools/tests/test_merge.py
index d5ddfe624e240..f27192dd3f379 100644
--- a/pandas/tools/tests/test_merge.py
+++ b/pandas/tools/tests/test_merge.py
@@ -459,13 +459,15 @@ def test_join_inner_multiindex(self):
         # _assert_same_contents(expected, expected2.ix[:, expected.columns])
 
     def test_join_hierarchical_mixed(self):
+        # GH 2024
         df = DataFrame([(1, 2, 3), (4, 5, 6)], columns=['a', 'b', 'c'])
         new_df = df.groupby(['a']).agg({'b': [np.mean, np.sum]})
         other_df = DataFrame(
             [(1, 2, 3), (7, 10, 6)], columns=['a', 'b', 'd'])
         other_df.set_index('a', inplace=True)
-
-        result = merge(new_df, other_df, left_index=True, right_index=True)
+        # GH 9455, 12219
+        with tm.assert_produces_warning(UserWarning):
+            result = merge(new_df, other_df, left_index=True, right_index=True)
         self.assertTrue(('b', 'mean') in result)
         self.assertTrue('b' in result)