diff --git a/doc/source/whatsnew/v1.1.0.rst b/doc/source/whatsnew/v1.1.0.rst
index 21e59805fa143..c00c5ac867f38 100644
--- a/doc/source/whatsnew/v1.1.0.rst
+++ b/doc/source/whatsnew/v1.1.0.rst
@@ -340,6 +340,7 @@ I/O
 - Bug in :class:`HDFStore` that caused it to set to ``int64`` the dtype of a ``datetime64`` column when reading a DataFrame in Python 3 from fixed format written in Python 2 (:issue:`31750`)
 - Bug in :meth:`read_excel` where a UTF-8 string with a high surrogate would cause a segmentation violation (:issue:`23809`)
 - Bug in :meth:`read_csv` was causing a file descriptor leak on an empty file (:issue:`31488`)
+- :meth:`HDFStore.keys` now tries to get the list of native pandas tables first, and if there are none, it gets the native HDF5 table names (:issue:`29916`)
 
 
 Plotting
diff --git a/pandas/io/pytables.py b/pandas/io/pytables.py
index 7aeed5c316d7f..916b3149f091e 100644
--- a/pandas/io/pytables.py
+++ b/pandas/io/pytables.py
@@ -583,13 +583,20 @@ def __exit__(self, exc_type, exc_value, traceback):
     def keys(self) -> List[str]:
         """
         Return a list of keys corresponding to objects stored in HDFStore.
+        If the store contains pandas native tables, it will return their names.
+        Otherwise the list of names of HDF5 Table objects will be returned.
 
         Returns
         -------
         list
             List of ABSOLUTE path-names (e.g. have the leading '/').
         """
-        return [n._v_pathname for n in self.groups()]
+        objects = [n._v_pathname for n in self.groups()]
+        if objects:
+            return objects
+
+        assert self._handle is not None  # mypy
+        return [n._v_pathname for n in self._handle.walk_nodes("/", classname="Table")]
 
     def __iter__(self):
         return iter(self.keys())
diff --git a/pandas/tests/io/pytables/test_store.py b/pandas/tests/io/pytables/test_store.py
index 61ca2e7f5f19d..e55c9157cac1f 100644
--- a/pandas/tests/io/pytables/test_store.py
+++ b/pandas/tests/io/pytables/test_store.py
@@ -296,6 +296,29 @@ def test_keys(self, setup_path):
             assert set(store.keys()) == expected
             assert set(store) == expected
 
+    def test_non_pandas_keys(self, setup_path):
+        # GH 29916
+        class Table1(tables.IsDescription):
+            value1 = tables.Float32Col()
+
+        class Table2(tables.IsDescription):
+            value2 = tables.Float32Col()
+
+        class Table3(tables.IsDescription):
+            value3 = tables.Float32Col()
+
+        with ensure_clean_path(setup_path) as path:
+            with tables.open_file(path, mode="w") as h5file:
+                group = h5file.create_group("/", "group")
+                h5file.create_table(group, "table1", Table1, "Table 1")
+                h5file.create_table(group, "table2", Table2, "Table 2")
+                h5file.create_table(group, "table3", Table3, "Table 3")
+            with HDFStore(path) as store:
+                assert len(store.keys()) == 3
+                expected = {"/group/table1", "/group/table2", "/group/table3"}
+                assert set(store.keys()) == expected
+                assert set(store) == expected
+
     def test_keys_ignore_hdf_softlink(self, setup_path):
 
         # GH 20523