diff --git a/packages/cli-snapshot/src/snapshot.js b/packages/cli-snapshot/src/snapshot.js
index e1c02f2d6..2a2ff9cbd 100644
--- a/packages/cli-snapshot/src/snapshot.js
+++ b/packages/cli-snapshot/src/snapshot.js
@@ -81,8 +81,8 @@ export const snapshot = command('snapshot', {
     if (file) {
       // load snapshots file
       let snapshots = yield loadSnapshotFile(file);
-      // accept a config object instead of an array of snapshots
-      let config = Array.isArray(snapshots) ? { snapshots } : snapshots;
+      // remove any references and accept an array of snapshots instead of an config object
+      let { references, ...config } = Array.isArray(snapshots) ? { snapshots } : snapshots;
       options = merge(config, { baseUrl, include, exclude });
     } else if (serve) {
       // serve and snapshot a static directory
diff --git a/packages/cli-snapshot/test/file.test.js b/packages/cli-snapshot/test/file.test.js
index ce9d089f3..706ef6956 100644
--- a/packages/cli-snapshot/test/file.test.js
+++ b/packages/cli-snapshot/test/file.test.js
@@ -224,4 +224,24 @@ describe('percy snapshot <file>', () => {
       '[percy] Error: No snapshots found'
     ]);
   });
+
+  it('allows a top-level references object for .yaml references', async () => {
+    fs.writeFileSync('references.yaml', [
+      'references:',
+      '  ref: &ref Reference Snapshot',
+      'snapshots:',
+      '  - url: http://localhost:8000/',
+      '    name: *ref'
+    ].join('\n'));
+
+    await snapshot(['./references.yaml']);
+
+    expect(logger.stderr).toEqual([]);
+    expect(logger.stdout).toEqual([
+      '[percy] Percy has started!',
+      '[percy] Snapshot taken: Reference Snapshot',
+      '[percy] Uploading 1 snapshot...',
+      '[percy] Finalized build #1: https://percy.io/test/test/123'
+    ]);
+  });
 });