diff --git a/changelog/4310.bugfix.rst b/changelog/4310.bugfix.rst
new file mode 100644
index 000000000..24e177c2e
--- /dev/null
+++ b/changelog/4310.bugfix.rst
@@ -0,0 +1 @@
+Fix duplicate collection due to multiple args matching the same packages.
diff --git a/src/_pytest/main.py b/src/_pytest/main.py
index 3c908ec4c..46228f824 100644
--- a/src/_pytest/main.py
+++ b/src/_pytest/main.py
@@ -387,6 +387,7 @@ class Session(nodes.FSCollector):
         self._initialpaths = frozenset()
         # Keep track of any collected nodes in here, so we don't duplicate fixtures
         self._node_cache = {}
+        self._collect_seen_pkgdirs = set()
 
         self.config.pluginmanager.register(self, name="session")
 
@@ -496,18 +497,19 @@ class Session(nodes.FSCollector):
         # and stack all Packages found on the way.
         # No point in finding packages when collecting doctests
         if not self.config.option.doctestmodules:
+            pm = self.config.pluginmanager
             for parent in argpath.parts():
-                pm = self.config.pluginmanager
                 if pm._confcutdir and pm._confcutdir.relto(parent):
                     continue
 
                 if parent.isdir():
                     pkginit = parent.join("__init__.py")
                     if pkginit.isfile():
+                        self._collect_seen_pkgdirs.add(parent)
                         if pkginit in self._node_cache:
                             root = self._node_cache[pkginit][0]
                         else:
-                            col = root._collectfile(pkginit)
+                            col = root._collectfile(pkginit, handle_dupes=False)
                             if col:
                                 if isinstance(col[0], Package):
                                     root = col[0]
@@ -529,13 +531,12 @@ class Session(nodes.FSCollector):
                 def filter_(f):
                     return f.check(file=1)
 
-            seen_dirs = set()
             for path in argpath.visit(
                 fil=filter_, rec=self._recurse, bf=True, sort=True
             ):
                 dirpath = path.dirpath()
-                if dirpath not in seen_dirs:
-                    seen_dirs.add(dirpath)
+                if dirpath not in self._collect_seen_pkgdirs:
+                    self._collect_seen_pkgdirs.add(dirpath)
                     pkginit = dirpath.join("__init__.py")
                     if pkginit.exists() and parts(pkginit.strpath).isdisjoint(paths):
                         for x in root._collectfile(pkginit):
@@ -570,20 +571,20 @@ class Session(nodes.FSCollector):
             for y in m:
                 yield y
 
-    def _collectfile(self, path):
+    def _collectfile(self, path, handle_dupes=True):
         ihook = self.gethookproxy(path)
         if not self.isinitpath(path):
             if ihook.pytest_ignore_collect(path=path, config=self.config):
                 return ()
 
-        # Skip duplicate paths.
-        keepduplicates = self.config.getoption("keepduplicates")
-        if not keepduplicates:
-            duplicate_paths = self.config.pluginmanager._duplicatepaths
-            if path in duplicate_paths:
-                return ()
-            else:
-                duplicate_paths.add(path)
+        if handle_dupes:
+            keepduplicates = self.config.getoption("keepduplicates")
+            if not keepduplicates:
+                duplicate_paths = self.config.pluginmanager._duplicatepaths
+                if path in duplicate_paths:
+                    return ()
+                else:
+                    duplicate_paths.add(path)
 
         return ihook.pytest_collect_file(path=path, parent=self)
 
diff --git a/src/_pytest/python.py b/src/_pytest/python.py
index 03a9fe031..d360e2c8f 100644
--- a/src/_pytest/python.py
+++ b/src/_pytest/python.py
@@ -545,11 +545,24 @@ class Package(Module):
             proxy = self.config.hook
         return proxy
 
-    def _collectfile(self, path):
+    def _collectfile(self, path, handle_dupes=True):
         ihook = self.gethookproxy(path)
         if not self.isinitpath(path):
             if ihook.pytest_ignore_collect(path=path, config=self.config):
                 return ()
+
+        if handle_dupes:
+            keepduplicates = self.config.getoption("keepduplicates")
+            if not keepduplicates:
+                duplicate_paths = self.config.pluginmanager._duplicatepaths
+                if path in duplicate_paths:
+                    return ()
+                else:
+                    duplicate_paths.add(path)
+
+        if self.fspath == path:  # __init__.py
+            return [self]
+
         return ihook.pytest_collect_file(path=path, parent=self)
 
     def isinitpath(self, path):
diff --git a/testing/test_collection.py b/testing/test_collection.py
index 3860cf9f9..dd8ecb1af 100644
--- a/testing/test_collection.py
+++ b/testing/test_collection.py
@@ -951,19 +951,35 @@ def test_collect_init_tests(testdir):
     result = testdir.runpytest(p, "--collect-only")
     result.stdout.fnmatch_lines(
         [
-            "*<Module '__init__.py'>",
-            "*<Function 'test_init'>",
-            "*<Module 'test_foo.py'>",
-            "*<Function 'test_foo'>",
+            "collected 2 items",
+            "<Package *",
+            "  <Module '__init__.py'>",
+            "    <Function 'test_init'>",
+            "  <Module 'test_foo.py'>",
+            "    <Function 'test_foo'>",
         ]
     )
     result = testdir.runpytest("./tests", "--collect-only")
     result.stdout.fnmatch_lines(
         [
-            "*<Module '__init__.py'>",
-            "*<Function 'test_init'>",
-            "*<Module 'test_foo.py'>",
-            "*<Function 'test_foo'>",
+            "collected 2 items",
+            "<Package *",
+            "  <Module '__init__.py'>",
+            "    <Function 'test_init'>",
+            "  <Module 'test_foo.py'>",
+            "    <Function 'test_foo'>",
+        ]
+    )
+    # Ignores duplicates with "." and pkginit (#4310).
+    result = testdir.runpytest("./tests", ".", "--collect-only")
+    result.stdout.fnmatch_lines(
+        [
+            "collected 2 items",
+            "<Package *",
+            "  <Module '__init__.py'>",
+            "    <Function 'test_init'>",
+            "  <Module 'test_foo.py'>",
+            "    <Function 'test_foo'>",
         ]
     )
     result = testdir.runpytest("./tests/test_foo.py", "--collect-only")