diff --git a/spec/project-spec.coffee b/spec/project-spec.coffee
index 976a5774b..956895952 100644
--- a/spec/project-spec.coffee
+++ b/spec/project-spec.coffee
@@ -352,6 +352,12 @@ describe "Project", ->
       expect(atom.project.getPaths()).toEqual(originalPaths)
       expect(onDidChangePathsSpy).not.toHaveBeenCalled()
 
+    it "doesn't destroy the repository if it is shared by another root directory", ->
+      atom.project.setPaths([__dirname, path.join(__dirname, "..", "src")])
+      atom.project.removePath(__dirname)
+      expect(atom.project.getPaths()).toEqual([path.join(__dirname, "..", "src")])
+      expect(atom.project.getRepositories()[0].isSubmodule("src")).toBe false
+
   describe ".relativize(path)", ->
     it "returns the path, relative to whichever root directory it is inside of", ->
       atom.project.addPath(temp.mkdirSync("another-path"))
diff --git a/src/project.coffee b/src/project.coffee
index 8844fa231..50bda3ed8 100644
--- a/src/project.coffee
+++ b/src/project.coffee
@@ -225,7 +225,7 @@ class Project extends Model
       [removedDirectory] = @rootDirectories.splice(indexToRemove, 1)
       [removedRepository] = @repositories.splice(indexToRemove, 1)
       removedDirectory.off()
-      removedRepository?.destroy()
+      removedRepository?.destroy() unless removedRepository in @repositories
       @emit "path-changed"
       @emitter.emit "did-change-paths", @getPaths()
       true