diff --git a/check/check-sysroot b/check/check-sysroot
index 7da415f..1950fad 100755
--- a/check/check-sysroot
+++ b/check/check-sysroot
@@ -36,3 +36,18 @@ run_test --cflags special-flags
 
 RESULT="-L$root/sysroot/foo -L$root/sysroot/bar -framework Foo -lsimple -framework Bar -Wl,-framework -Wl,Baz"
 run_test --libs special-flags
+
+# packages from different locations gets the same /sysroot prefix
+export PKG_CONFIG_PATH="${srcdir}/sub"
+RESULT="-I/sysroot/sub/include -I/sysroot/public-dep/include"
+run_test --cflags  public-dep sub1
+
+# Map sub1 location to another sysroot
+if [ "$native_win32" = yes ]; then
+    export PKG_CONFIG_SYSROOT_MAP="${srcdir}/sub;/subsysroot"
+else
+    export PKG_CONFIG_SYSROOT_MAP="${srcdir}/sub:/subsysroot"
+fi
+
+RESULT="-I/subsysroot/sub/include -I/sysroot/public-dep/include"
+run_test --cflags public-dep sub1
diff --git a/main.c b/main.c
index 9b27d9a..ed2c2f5 100644
--- a/main.c
+++ b/main.c
@@ -489,6 +489,7 @@ main (int argc, char **argv)
   GList *packages = NULL;
   char *search_path;
   char *pcbuilddir;
+  char *pcsysrootmap;
   gboolean need_newline;
   FILE *log = NULL;
   GError *error = NULL;
@@ -541,6 +542,12 @@ main (int argc, char **argv)
       define_global_variable ("pc_sysrootdir", "/");
     }
 
+  pcsysrootmap = getenv ("PKG_CONFIG_SYSROOT_MAP");
+  if (pcsysrootmap)
+    {
+      add_sysroot_map (pcsysrootmap, G_SEARCHPATH_SEPARATOR_S);
+    }
+
   pcbuilddir = getenv ("PKG_CONFIG_TOP_BUILD_DIR");
   if (pcbuilddir)
     {
diff --git a/parse.c b/parse.c
index 6e9907c..bf8c412 100644
--- a/parse.c
+++ b/parse.c
@@ -640,6 +640,8 @@ static void _do_parse_libs (Package *pkg, int argc, char **argv)
       p = arg;
       g_free(tmp);
 
+      flag->pkg = pkg;
+
       if (p[0] == '-' &&
           p[1] == 'l' &&
 	  /* -lib: is used by the C# compiler for libs; it's not an -l
@@ -842,6 +844,8 @@ parse_cflags (Package *pkg, const char *str, const char *path)
       char *p = arg;
       g_free(tmp);
 
+      flag->pkg = pkg;
+
       if (p[0] == '-' &&
           p[1] == 'I')
         {
diff --git a/pkg-config.1 b/pkg-config.1
index a147fc8..9643822 100644
--- a/pkg-config.1
+++ b/pkg-config.1
@@ -368,6 +368,13 @@ to determine CFLAGS and LDFLAGS. -I and -L are modified to point to
 the new system root. this means that a -I/usr/include/libfoo will
 become -I/var/target/usr/include/libfoo with a PKG_CONFIG_SYSROOT_DIR
 equal to /var/target (same rule apply to -L)
+.I "PKG_CONFIG_SYSROOT_MAP"
+Similar to PKG_CONFIG_SYSROOT_DIR but allow mapping location where the pc file
+was found to a sysroot. A colon-separated (on Windows, semicolon-separated) list
+that gets splitted in pairs where the first path is the location of package file
+(usually part of PKG_CONFIG_LIBDIR or PKG_CONFIG_PATH) and the second path is
+the sysroot. For example:
+PKG_CONFIG_SYSROOT_MAP=/sysroot/usr/lib/pkgconfig:/sysroot:/sysroot2/usr/lib/pkgconfig:/sysroot2
 .TP
 .I "PKG_CONFIG_LIBDIR"
 Replaces the default
diff --git a/pkg.c b/pkg.c
index f29ecc7..fcd2d60 100644
--- a/pkg.c
+++ b/pkg.c
@@ -45,6 +45,7 @@ static void verify_package (Package *pkg);
 static GHashTable *packages = NULL;
 static GHashTable *globals = NULL;
 static GList *search_dirs = NULL;
+static GHashTable *sysroot_map = NULL;
 
 gboolean disable_uninstalled = FALSE;
 gboolean ignore_requires = FALSE;
@@ -78,6 +79,36 @@ add_search_dirs (const char *path, const char *separator)
       g_strfreev (search_dirs);
 }
 
+void
+add_sysroot_map (const char *path, const char *separator)
+{
+  char **strv;
+  char **iter;
+
+  if (sysroot_map == NULL)
+    sysroot_map = g_hash_table_new (g_str_hash, g_str_equal);
+
+  strv = g_strsplit (path, separator, -1);
+
+  iter = strv;
+  while (*iter)
+    {
+      char *pcfiledir = *iter++;
+      char *sysroot = *iter++;
+
+      if (sysroot == NULL) {
+        verbose_error ("PKG_CONFIG_SYSROOT_MAP must contain even number of paths.");
+        exit (1);
+      }
+
+      debug_spew ("Adding sysroot map '%s' -> '%s' from PKG_CONFIG_SYSROOT_MAP\n",
+                  pcfiledir, sysroot);
+      g_hash_table_insert(sysroot_map, pcfiledir, sysroot);
+    }
+
+  g_free (strv);
+}
+
 #ifdef G_OS_WIN32
 /* Guard against .pc file being installed with UPPER CASE name */
 # define FOLD(x) tolower(x)
@@ -393,47 +424,33 @@ get_package_quiet (const char *name)
   return internal_get_package (name, FALSE);
 }
 
-/* Strip consecutive duplicate arguments in the flag list. */
-static GList *
-flag_list_strip_duplicates (GList *list)
-{
-  GList *tmp;
-
-  /* Start at the 2nd element of the list so we don't have to check for an
-   * existing previous element. */
-  for (tmp = g_list_next (list); tmp != NULL; tmp = g_list_next (tmp))
-    {
-      Flag *cur = tmp->data;
-      Flag *prev = tmp->prev->data;
-
-      if (cur->type == prev->type && g_strcmp0 (cur->arg, prev->arg) == 0)
-        {
-          /* Remove the duplicate flag from the list and move to the last
-           * element to prepare for the next iteration. */
-          GList *dup = tmp;
-
-          debug_spew (" removing duplicate \"%s\"\n", cur->arg);
-          tmp = g_list_previous (tmp);
-          list = g_list_remove_link (list, dup);
-        }
-    }
-
-  return list;
-}
-
 static char *
 flag_list_to_string (GList *list)
 {
   GList *tmp;
   GString *str = g_string_new ("");
   char *retval;
-  
+  gsize prev_arg_len = 0;
+  FlagType prev_type = 0;
+
+  if (sysroot_map == NULL)
+    sysroot_map = g_hash_table_new (g_str_hash, g_str_equal);
+
   tmp = list;
   while (tmp != NULL) {
     Flag *flag = tmp->data;
     char *tmpstr = flag->arg;
+    char *sysroot;
+    char *cur_arg;
+    char *prev_arg;
+    gsize cur_arg_len;
+    gsize old_len = str->len;
 
-    if (pcsysrootdir != NULL && flag->type & (CFLAGS_I | LIBS_L)) {
+    sysroot = g_hash_table_lookup (sysroot_map, flag->pkg->pcfiledir);
+    if (sysroot == NULL)
+      sysroot = pcsysrootdir;
+
+    if (sysroot != NULL && flag->type & (CFLAGS_I | LIBS_L)) {
       /* Handle non-I Cflags like -isystem */
       if (flag->type & CFLAGS_I && strncmp (tmpstr, "-I", 2) != 0) {
         char *space = strchr (tmpstr, ' ');
@@ -441,18 +458,33 @@ flag_list_to_string (GList *list)
         /* Ensure this has a separate arg */
         g_assert (space != NULL && space[1] != '\0');
         g_string_append_len (str, tmpstr, space - tmpstr + 1);
-        g_string_append (str, pcsysrootdir);
+        g_string_append (str, sysroot);
         g_string_append (str, space + 1);
       } else {
         g_string_append_c (str, '-');
         g_string_append_c (str, tmpstr[1]);
-        g_string_append (str, pcsysrootdir);
+        g_string_append (str, sysroot);
         g_string_append (str, tmpstr+2);
       }
     } else {
       g_string_append (str, tmpstr);
     }
     g_string_append_c (str, ' ');
+
+    /* truncate the string if the arg we added is identical to the previous one */
+    cur_arg = str->str + old_len;
+    cur_arg_len = str->len - old_len;
+    prev_arg = cur_arg - prev_arg_len;
+    if (prev_type == flag->type && prev_arg_len == cur_arg_len && strncmp(cur_arg, prev_arg, cur_arg_len) == 0)
+      {
+        g_string_truncate (str, old_len);
+      }
+    else
+      {
+        prev_type = flag->type;
+        prev_arg_len = cur_arg_len;
+      }
+
     tmp = g_list_next (tmp);
   }
 
@@ -918,7 +950,6 @@ get_multi_merged (GList *pkgs, FlagType type, gboolean in_path_order,
   char *retval;
 
   list = fill_list (pkgs, type, in_path_order, include_private);
-  list = flag_list_strip_duplicates (list);
   retval = flag_list_to_string (list);
   g_list_free (list);
 
diff --git a/pkg.h b/pkg.h
index c6732bd..c85ddd8 100644
--- a/pkg.h
+++ b/pkg.h
@@ -53,6 +53,7 @@ struct Flag_
 {
   FlagType type;
   char *arg;
+  Package *pkg;
 };
 
 struct RequiredVersion_
@@ -98,6 +99,7 @@ char *   packages_get_var          (GList      *pkgs,
 
 void add_search_dir (const char *path);
 void add_search_dirs (const char *path, const char *separator);
+void add_sysroot_map (const char *path, const char *separator);
 void package_init (gboolean want_list);
 int compare_versions (const char * a, const char *b);
 gboolean version_test (ComparisonType comparison,