diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index b0b2701c27a..9ff7ef7c0c7 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -27,11 +27,15 @@ Changes
 * Change exception raised by ``capture.DontReadFromInput.fileno()`` from ``ValueError`` 
   to ``io.UnsupportedOperation``. Thanks `@vlad-dragos`_ for the PR.
 
+* Fix an internal caching issue which could cause hooks from ``conftest.py`` files in
+  sub-directories to be called in other directories incorrectly (`#2016`_).
+  Thanks `@d-b-w`_ for the report and `@nicoddemus`_ for the PR.
 
-* fix `#2013`_: turn RecordedWarning into namedtupe,
-  to give it a comprehensible repr while preventing unwarranted modification
+* fix `#2013`_: turn RecordedWarning into ``namedtuple``
+  to give it a comprehensible repr while preventing unwarranted modification.
 
 .. _@davidszotten: https://github.com/davidszotten
+.. _@d-b-w: https://github.com/d-b-w
 .. _@fushi: https://github.com/fushi
 .. _@mattduck: https://github.com/mattduck
 
@@ -39,6 +43,7 @@ Changes
 .. _#1874: https://github.com/pytest-dev/pytest/pull/1874
 .. _#1952: https://github.com/pytest-dev/pytest/pull/1952
 .. _#2013: https://github.com/pytest-dev/pytest/issues/2013
+.. _#2016: https://github.com/pytest-dev/pytest/issues/2016
 
 
 3.0.5.dev0
diff --git a/_pytest/main.py b/_pytest/main.py
index 451355ef3e4..fc1a3c20460 100644
--- a/_pytest/main.py
+++ b/_pytest/main.py
@@ -561,7 +561,20 @@ def pytest_runtest_logreport(self, report):
     def isinitpath(self, path):
         return path in self._initialpaths
 
+    def _maybe_clear_hook_proxy_cache(self):
+        """
+        Reset the hook proxy cache if the number of conftests has changed
+        since the last time it was used (#2016).
+        """
+        pm = self.config.pluginmanager
+        total_conftests = len(pm._conftest_plugins)
+        last_conftests = getattr(self, 'last_conftests', 0)
+        if total_conftests != last_conftests:
+            self._fs2hookproxy.clear()
+            self.last_conftests = total_conftests
+
     def gethookproxy(self, fspath):
+        self._maybe_clear_hook_proxy_cache()
         try:
             return self._fs2hookproxy[fspath]
         except KeyError:
diff --git a/_pytest/pytester.py b/_pytest/pytester.py
index 641c7c31f51..dce5c3618fc 100644
--- a/_pytest/pytester.py
+++ b/_pytest/pytester.py
@@ -481,6 +481,7 @@ def _makefile(self, ext, args, kwargs):
         ret = None
         for name, value in items:
             p = self.tmpdir.join(name).new(ext=ext)
+            p.dirpath().ensure_dir()
             source = Source(value)
             def my_totext(s, encoding="utf-8"):
                 if py.builtin._isbytes(s):
diff --git a/testing/test_conftest.py b/testing/test_conftest.py
index 377283eb92d..d50d1fa5f13 100644
--- a/testing/test_conftest.py
+++ b/testing/test_conftest.py
@@ -421,3 +421,26 @@ def test_some():
     res = testdir.runpytest()
     assert res.ret == 4
     assert 'raise ValueError()' in [line.strip() for line in res.errlines]
+
+
+def test_hook_proxy_cache(testdir):
+    """Session's gethookproxy() could cache incorrectly conftests (#2016)."""
+    testdir.makepyfile(**{
+        'root/demo-0/test_foo1.py': "def test1(): pass",
+
+        'root/demo-a/test_foo2.py': "def test1(): pass",
+        'root/demo-a/conftest.py': """
+            def pytest_ignore_collect(path, config):
+                return True
+            """,
+
+        'root/demo-b/test_foo3.py': "def test1(): pass",
+        'root/demo-c/test_foo4.py': "def test1(): pass",
+    })
+    result = testdir.runpytest()
+    result.stdout.fnmatch_lines([
+        '*test_foo1.py*',
+        '*test_foo3.py*',
+        '*test_foo4.py*',
+        '*3 passed*',
+    ])
diff --git a/testing/test_pluginmanager.py b/testing/test_pluginmanager.py
index e61c84247c3..22f02cb4736 100644
--- a/testing/test_pluginmanager.py
+++ b/testing/test_pluginmanager.py
@@ -4,7 +4,8 @@
 import os
 
 from _pytest.config import get_config, PytestPluginManager
-from _pytest.main import EXIT_NOTESTSCOLLECTED
+from _pytest.main import EXIT_NOTESTSCOLLECTED, Session
+
 
 @pytest.fixture
 def pytestpm():
@@ -129,6 +130,25 @@ def pytest_plugin_registered(self):
         finally:
             undo()
 
+    def test_hook_proxy_cache_reset(self, testdir):
+        """Importing new conftest files should reset the internal hook proxy cache (#2016)"""
+        config = testdir.parseconfig()
+        session = Session(config)
+        testdir.makepyfile(**{
+            'tests/conftest.py': '',
+            'tests/subdir/conftest.py': '',
+        })
+
+        conftest1 = testdir.tmpdir.join('tests/conftest.py')
+        conftest2 = testdir.tmpdir.join('tests/subdir/conftest.py')
+
+        config.pluginmanager._importconftest(conftest1)
+        ihook_a = session.gethookproxy(testdir.tmpdir.join('tests'))
+        assert ihook_a is not None
+        config.pluginmanager._importconftest(conftest2)
+        ihook_b = session.gethookproxy(testdir.tmpdir.join('tests'))
+        assert ihook_a is not ihook_b
+
     def test_warn_on_deprecated_multicall(self, pytestpm):
         warnings = []