BUG: rename with Series with non-unique index

doc/source/whatsnew/v3.0.0.rst

@@ -1236,6 +1236,7 @@ Other
 - Bug in :meth:`DataFrame.query` where using duplicate column names led to a ``TypeError``. (:issue:`59950`)
 - Bug in :meth:`DataFrame.query` which raised an exception or produced incorrect results when expressions contained backtick-quoted column names containing the hash character ``#``, backticks, or characters that fall outside the ASCII range (U+0001..U+007F). (:issue:`59285`) (:issue:`49633`)
 - Bug in :meth:`DataFrame.query` which raised an exception when querying integer column names using backticks. (:issue:`60494`)
+- Bug in :meth:`DataFrame.rename` and :meth:`Series.rename` when passed a ``mapper``, ``index``, or ``columns`` argument that is a :class:`Series` with non-unique ``ser.index`` producing a corrupted result instead of raising ``ValueError`` (:issue:`58621`)
 - Bug in :meth:`DataFrame.sample` with ``replace=False`` and ``(n * max(weights) / sum(weights)) > 1``, the method would return biased results. Now raises ``ValueError``. (:issue:`61516`)
 - Bug in :meth:`DataFrame.shift` where passing a ``freq`` on a DataFrame with no columns did not shift the index correctly. (:issue:`60102`)
 - Bug in :meth:`DataFrame.sort_index` when passing ``axis="columns"`` and ``ignore_index=True`` and ``ascending=False`` not returning a :class:`RangeIndex` columns (:issue:`57293`)

pandas/core/generic.py

@@ -1054,6 +1054,10 @@ def _rename(
             if level is not None:
                 level = ax._get_level_number(level)
 
+            if isinstance(replacements, ABCSeries) and not replacements.index.is_unique:
+                # GH#58621
+                raise ValueError("Cannot rename with a Series with non-unique index.")
+
             # GH 13473
             if not callable(replacements):
                 if ax._is_multi and level is not None:

pandas/tests/frame/methods/test_rename.py

@@ -8,6 +8,7 @@
     DataFrame,
     Index,
     MultiIndex,
+    Series,
     merge,
 )
 import pandas._testing as tm
@@ -409,3 +410,33 @@ def test_rename_boolean_index(self):
             index=["foo", "bar", "bah"],
         )
         tm.assert_frame_equal(res, exp)
+
+    def test_rename_non_unique_index_series(self):
+        # GH#58621
+        df = DataFrame({"A": [1, 2, 3], "B": [4, 5, 6], "C": [7, 8, 9]})
+        orig = df.copy(deep=True)
+
+        rename_series = Series(["X", "Y", "Z", "W"], index=["A", "B", "B", "C"])
+
+        msg = "Cannot rename with a Series with non-unique index"
+        with pytest.raises(ValueError, match=msg):
+            df.rename(rename_series)
+        with pytest.raises(ValueError, match=msg):
+            df.rename(columns=rename_series)
+        with pytest.raises(ValueError, match=msg):
+            df.rename(columns=rename_series, inplace=True)
+
+        # check we didn't corrupt the original
+        tm.assert_frame_equal(df, orig)
+
+        # Check the Series method while we're here
+        ser = df.iloc[0]
+        with pytest.raises(ValueError, match=msg):
+            ser.rename(rename_series)
+        with pytest.raises(ValueError, match=msg):
+            ser.rename(index=rename_series)
+        with pytest.raises(ValueError, match=msg):
+            ser.rename(index=rename_series, inplace=True)
+
+        # check we didn't corrupt the original
+        tm.assert_series_equal(ser, orig.iloc[0])