diff --git a/geopandas/geodataframe.py b/geopandas/geodataframe.py
index 4c74bac..acf4f4a 100644
--- a/geopandas/geodataframe.py
+++ b/geopandas/geodataframe.py
@@ -113,9 +113,7 @@ class GeoDataFrame(GeoPandasBase, DataFrame):
 
         to_remove = None
         geo_column_name = DEFAULT_GEO_COLUMN_NAME
-        if isinstance(col, Series):
-            level = col.values
-        elif isinstance(col, (list, np.ndarray)):
+        if isinstance(col, (Series, list, np.ndarray)):
             level = col
         elif hasattr(col, 'ndim') and col.ndim != 1:
             raise ValueError("Must pass array with one dimension only.")
diff --git a/tests/test_geodataframe.py b/tests/test_geodataframe.py
index 2d5f60f..d5ca1b5 100644
--- a/tests/test_geodataframe.py
+++ b/tests/test_geodataframe.py
@@ -182,6 +182,27 @@ class TestDataFrame(unittest.TestCase):
         geom = GeoSeries(geom, index=self.df.index, crs=self.df.crs)
         assert_geoseries_equal(self.df.geometry, geom)
 
+    def test_set_geometry_series(self):
+        # Test when setting geometry with a Series that
+        # alignment will occur
+        #
+        # Reverse the index order
+        # Set the Series to be Point(i,i) where i is the index
+        self.df.index = range(len(self.df)-1, -1, -1)
+
+        d = {}
+        for i in range(len(self.df)):
+            d[i] = Point(i, i)
+        g = GeoSeries(d)
+        # At this point, the DataFrame index is [4,3,2,1,0] and the
+        # GeoSeries index is [0,1,2,3,4]. Make sure set_geometry aligns
+        # them to match indexes
+        df = self.df.set_geometry(g)
+
+        for i, r in df.iterrows():
+            self.assertAlmostEqual(i, r['geometry'].x)
+            self.assertAlmostEqual(i, r['geometry'].y)
+
     def test_to_json(self):
         text = self.df.to_json()
         data = json.loads(text)