diff --git a/packages/babel-core/src/helpers/merge.js b/packages/babel-core/src/helpers/merge.js
index 71eacdbf2c..962f255926 100644
--- a/packages/babel-core/src/helpers/merge.js
+++ b/packages/babel-core/src/helpers/merge.js
@@ -7,13 +7,15 @@ export default function (dest?: Object, src?: Object): ?Object {
 
   return merge(dest, src, function (a, b) {
     if (b && Array.isArray(a)) {
-      let c = a.slice(0);
-      for (let v of b) {
-        if (a.indexOf(v) < 0) {
-          c.push(v);
+      let newArray = b.slice(0);
+
+      for (let item of a) {
+        if (newArray.indexOf(item) < 0) {
+          newArray.push(item);
         }
       }
-      return c;
+
+      return newArray;
     }
   });
 }
diff --git a/packages/babel-core/test/api.js b/packages/babel-core/test/api.js
index c4e615de7a..f781bab8bf 100644
--- a/packages/babel-core/test/api.js
+++ b/packages/babel-core/test/api.js
@@ -24,6 +24,15 @@ function transformAsync(code, opts) {
 }
 
 suite("api", function () {
+  test("options merge backwards", function () {
+    return transformAsync("", {
+      presets: [__dirname + "/../../babel-preset-es2015"],
+      plugins: [__dirname + "/../../babel-plugin-syntax-jsx"]
+    }).then(function (result) {
+      assert.ok(result.options.plugins[0][0].manipulateOptions.toString().indexOf("jsx") >= 0);
+    });
+  });
+
   test("code option false", function () {
     return transformAsync("foo('bar');", { code: false }).then(function (result) {
       assert.ok(!result.code);