diff --git a/packages/jest-cli/src/__tests__/search_source.test.js b/packages/jest-cli/src/__tests__/search_source.test.js
index f611865a72d5..d42787540544 100644
--- a/packages/jest-cli/src/__tests__/search_source.test.js
+++ b/packages/jest-cli/src/__tests__/search_source.test.js
@@ -463,5 +463,24 @@ describe('SearchSource', () => {
         path.join(rootDir, '__testtests__', 'test.jsx'),
       ]);
     });
+
+    it('does not mistake roots folders with prefix names', async () => {
+      const config = normalize(
+        {
+          name,
+          rootDir: '.',
+          roots: ['/foo/bar/prefix'],
+        },
+        {},
+      ).options;
+
+      searchSource = new SearchSource(
+        await Runtime.createContext(config, {maxWorkers}),
+      );
+
+      const input = ['/foo/bar/prefix-suffix/__tests__/my-test.test.js'];
+      const data = searchSource.findTestsByPaths(input);
+      expect(data.tests).toEqual([]);
+    });
   });
 });
diff --git a/packages/jest-cli/src/search_source.js b/packages/jest-cli/src/search_source.js
index d20bb18ef264..6f153467be58 100644
--- a/packages/jest-cli/src/search_source.js
+++ b/packages/jest-cli/src/search_source.js
@@ -78,7 +78,7 @@ export default class SearchSource {
     const {config} = context;
     this._context = context;
     this._rootPattern = new RegExp(
-      config.roots.map(dir => escapePathForRegex(dir)).join('|'),
+      config.roots.map(dir => escapePathForRegex(dir + path.sep)).join('|'),
     );
 
     const ignorePattern = config.testPathIgnorePatterns;