diff --git a/pip/req/req_install.py b/pip/req/req_install.py

index 6911fba..8524932 100644

--- a/pip/req/req_install.py

+++ b/pip/req/req_install.py

@@ -34,7 +34,7 @@ from pip.locations import (

 )

 from pip.utils import (

     display_path, rmtree, ask_path_exists, backup_dir, is_installable_dir,

-    dist_in_usersite, dist_in_site_packages, egg_link_path,

+    dist_in_usersite, dist_in_site_packages, dist_in_install_path, egg_link_path,

     call_subprocess, read_text_file, FakeFile, _make_build_dir, ensure_dir,

     get_installed_version, normalize_path, dist_is_local,

 )

@@ -1049,7 +1049,7 @@ class InstallRequirement(object):

                         "lack sys.path precedence to %s in %s" %

                         (existing_dist.project_name, existing_dist.location)

                     )

-            else:

+            elif dist_in_install_path(existing_dist):

                 self.conflicts_with = existing_dist

         return True

diff --git a/pip/req/req_set.py b/pip/req/req_set.py

index 76aec06..b93304a 100644

--- a/pip/req/req_set.py

+++ b/pip/req/req_set.py

@@ -18,7 +18,8 @@ from pip.exceptions import (InstallationError, BestVersionAlreadyInstalled,

                             UnsupportedPythonVersion)

 from pip.req.req_install import InstallRequirement

 from pip.utils import (

-    display_path, dist_in_usersite, ensure_dir, normalize_path)

+    display_path, dist_in_usersite, dist_in_install_path, ensure_dir,

+    normalize_path)

 from pip.utils.hashes import MissingHashes

 from pip.utils.logging import indent_log

 from pip.utils.packaging import check_dist_requires_python

@@ -437,10 +438,12 @@ class RequirementSet(object):

                 if not best_installed:

                     # don't uninstall conflict if user install and

-                    # conflict is not user install

+                    # conflict is not user install or conflict lives

+                    # in a different path (/usr/lib vs /usr/local/lib/)

                     if not (self.use_user_site and not

-                            dist_in_usersite(req_to_install.satisfied_by)):

-                        req_to_install.conflicts_with = \

+                            dist_in_usersite(req_to_install.satisfied_by) or not

+                            dist_in_install_path(req_to_install.satisfied_by)):

+                        req_to_install.conflicts_with = \

                             req_to_install.satisfied_by

                     req_to_install.satisfied_by = None

@@ -644,10 +647,12 @@ class RequirementSet(object):

                 if req_to_install.satisfied_by:

                     if self.upgrade or self.ignore_installed:

                         # don't uninstall conflict if user install and

-                        # conflict is not user install

+                        # conflict is not user install or conflict lives

+                        # in a different path (/usr/lib vs /usr/local/lib/)

                         if not (self.use_user_site and not

                                 dist_in_usersite(

-                                    req_to_install.satisfied_by)):

+                                    req_to_install.satisfied_by) or not

+                                dist_in_install_path(req_to_install.satisfied_by)):

                             req_to_install.conflicts_with = \

                                 req_to_install.satisfied_by

                         req_to_install.satisfied_by = None

diff --git a/pip/utils/__init__.py b/pip/utils/__init__.py

index 815bd33..0ed59f7 100644

--- a/pip/utils/__init__.py

+++ b/pip/utils/__init__.py

@@ -22,7 +22,7 @@ from pip.exceptions import InstallationError

 from pip.compat import console_to_str, expanduser, stdlib_pkgs

 from pip.locations import (

     site_packages, user_site, running_under_virtualenv, virtualenv_no_global,

-    write_delete_marker_file,

+    write_delete_marker_file, distutils_scheme,

 )

 from pip._vendor import pkg_resources

 from pip._vendor.six.moves import input

@@ -315,6 +315,16 @@ def dist_in_site_packages(dist):

     ).startswith(normalize_path(site_packages))

+def dist_in_install_path(dist):

+    """

+    Return True if given Distribution is installed in

+    path matching distutils_scheme layout.

+    """

+    norm_path = normalize_path(dist_location(dist))

+    return norm_path.startswith(normalize_path(

+        distutils_scheme("")['purelib'].split('python')[0]))

+

+

 def dist_is_editable(dist):

     """Is distribution an editable install?"""

     for path_item in sys.path: