diff --git a/js/data/feature_tree.js b/js/data/feature_tree.js
index da75a94f9ea..4e80ec96175 100644
--- a/js/data/feature_tree.js
+++ b/js/data/feature_tree.js
@@ -14,8 +14,8 @@ function FeatureTree(getGeometry, getType) {
     this.toBeInserted = [];
 }
 
-FeatureTree.prototype.insert = function(bbox, layer, feature) {
-    bbox.layer = layer;
+FeatureTree.prototype.insert = function(bbox, layers, feature) {
+    bbox.layers = layers;
     bbox.feature = feature;
     this.toBeInserted.push(bbox);
 };
@@ -42,7 +42,7 @@ FeatureTree.prototype.query = function(args, callback) {
         var type = this.getType(feature);
         var geometry = this.getGeometry(feature);
 
-        if (params.layer && matching[i].layer.id !== params.layer.id)
+        if (params.layer && matching[i].layers.indexOf(params.layer.id) < 0)
             continue;
         if (params.$type && type !== params.$type)
             continue;
@@ -52,7 +52,7 @@ FeatureTree.prototype.query = function(args, callback) {
         var props = {
             $type: type,
             properties: matching[i].feature.properties,
-            layer: matching[i].layer
+            layers: matching[i].layers
         };
 
         if (params.geometry) {
diff --git a/js/source/worker_tile.js b/js/source/worker_tile.js
index 775fe5cb329..a5bb4e04bb1 100644
--- a/js/source/worker_tile.js
+++ b/js/source/worker_tile.js
@@ -56,6 +56,7 @@ WorkerTile.prototype.parse = function(data, layers, actor, callback) {
             continue;
 
         bucket = createBucket(layer, buffers, collision);
+        bucket.layers = [layer.id];
 
         buckets[bucket.id] = bucket;
         bucketsInOrder.push(bucket);
@@ -72,6 +73,19 @@ WorkerTile.prototype.parse = function(data, layers, actor, callback) {
         }
     }
 
+    // Index ref layers.
+    for (i = 0; i < layers.length; i++) {
+        layer = layers[i];
+
+        if (layer.source !== this.source)
+            continue;
+
+        if (!layer.ref)
+            continue;
+
+        buckets[layer.ref].layers.push(layer.id);
+    }
+
     // read each layer, and sort its features into buckets
     if (data.layers) {
         // vectortile
@@ -150,7 +164,7 @@ WorkerTile.prototype.parse = function(data, layers, actor, callback) {
             if (bucket.interactive) {
                 for (var i = 0; i < bucket.features.length; i++) {
                     var feature = bucket.features[i];
-                    tile.featureTree.insert(feature.bbox(), {id: bucket.id}, feature);
+                    tile.featureTree.insert(feature.bbox(), bucket.layers, feature);
                 }
             }
             if (typeof self !== 'undefined') {
diff --git a/js/style/style.js b/js/style/style.js
index 9935522d8fc..6b0b6a2a312 100644
--- a/js/style/style.js
+++ b/js/style/style.js
@@ -123,7 +123,7 @@ Style.prototype = util.inherit(Evented, {
         for (id in this._layers) {
             layer = this._layers[id];
 
-            ordered.push(layer.transferable());
+            ordered.push(layer.json());
 
             if (layer.nested)
                 continue;
@@ -241,11 +241,9 @@ Style.prototype = util.inherit(Evented, {
         }, () => {
             if (error) return callback(error);
 
-            features.forEach((feature) => {
-                var layer = this._layers[feature.layer.id];
-                util.extend(feature.layer, layer._layer, {
-                    paint: layer.paint,
-                    layout: layer.layout
+            features.forEach(feature => {
+                feature.layers = feature.layers.map(id => {
+                    return this._layers[id].json();
                 });
             });
 
diff --git a/js/style/style_layer.js b/js/style/style_layer.js
index 25dc9558fec..801a31dea06 100644
--- a/js/style/style_layer.js
+++ b/js/style/style_layer.js
@@ -19,16 +19,6 @@ function StyleLayer(layer) {
 }
 
 StyleLayer.prototype = {
-    assign(layer) {
-        this.type            = layer.type;
-        this.source          = layer.source;
-        this['source-layer'] = layer['source-layer'];
-        this.minzoom         = layer.minzoom;
-        this.maxzoom         = layer.maxzoom;
-        this.filter          = layer.filter;
-        this.layout          = layer.layout;
-    },
-
     resolveLayout(layers, constants) {
         if (!this.ref) {
             this.layout = new LayoutProperties[this.type](
@@ -144,8 +134,20 @@ StyleLayer.prototype = {
         return !this.hidden;
     },
 
-    transferable() {
-        return util.extend({}, this._layer, {layout: this.layout});
+    assign(layer) {
+        util.extend(this, util.pick(layer,
+            'type', 'source', 'source-layer',
+            'minzoom', 'maxzoom', 'filter',
+            'layout'));
+    },
+
+    json() {
+        return util.extend({},
+            this._layer,
+            util.pick(this,
+                'type', 'source', 'source-layer',
+                'minzoom', 'maxzoom', 'filter',
+                'layout', 'paint'));
     }
 };
 
diff --git a/test/js/data/feature_tree.test.js b/test/js/data/feature_tree.test.js
index d6f2c225571..284bed9d1b1 100644
--- a/test/js/data/feature_tree.test.js
+++ b/test/js/data/feature_tree.test.js
@@ -71,7 +71,7 @@ test('featuretree query', function(t) {
 
     for (var i=0; i<tile.layers.water._features.length; i++) {
         var feature = tile.layers.water.feature(i);
-        ft.insert(feature.bbox(), {id: 'water'}, feature);
+        ft.insert(feature.bbox(), ['water'], feature);
     }
 
     ft.query({
@@ -86,8 +86,7 @@ test('featuretree query', function(t) {
         t.notEqual(features.length, 0, 'non-empty results for queryFeatures');
         features.forEach(function(f) {
             t.ok(f.$type, 'result has $type');
-            t.ok(f.layer, 'result has layer');
-            t.equal(f.layer.id, 'water');
+            t.deepEqual(f.layers, ['water']);
             t.ok(f.properties, 'result has properties');
             t.notEqual(f.properties.osm_id, undefined, 'properties has osm_id by default');
         });
diff --git a/test/js/style/style.test.js b/test/js/style/style.test.js
index e38d9fe55b2..060f97ae178 100644
--- a/test/js/style/style.test.js
+++ b/test/js/style/style.test.js
@@ -261,20 +261,10 @@ test('Style#featuresAt', function(t) {
         style.sources.mapbox.featuresAt = function(position, params, callback) {
             callback(null, [{
                 $type: 'Polygon',
-                layer: {
-                    id: 'land',
-                    type: 'line'
-                }
+                layers: ['land']
             }, {
                 $type: 'Polygon',
-                layer: {
-                    id: 'landref',
-                    ref: 'land',
-                    type: 'line',
-                    paint: {
-                        'line-color': 'blue'
-                    }
-                }
+                layers: ['land', 'landref']
             }]);
         };
 
@@ -290,7 +280,7 @@ test('Style#featuresAt', function(t) {
             style.featuresAt([256, 256], {}, function(err, results) {
                 t.error(err);
 
-                var layout = results[0].layer.layout;
+                var layout = results[0].layers[0].layout;
                 t.deepEqual(layout, {'line-cap': 'round'});
                 t.deepEqual(
                     Object.getPrototypeOf(layout),
@@ -304,7 +294,7 @@ test('Style#featuresAt', function(t) {
             style.featuresAt([256, 256], {}, function(err, results) {
                 t.error(err);
 
-                var paint = results[0].layer.paint;
+                var paint = results[0].layers[0].paint;
                 t.deepEqual(paint, {'line-color': [ 1, 0, 0, 1 ]});
                 t.deepEqual(
                     Object.getPrototypeOf(paint),
@@ -318,8 +308,8 @@ test('Style#featuresAt', function(t) {
             style.featuresAt([256, 256], {}, function(err, results) {
                 t.error(err);
 
-                var layer = results[0].layer;
-                var refLayer = results[1].layer;
+                var layer = results[1].layers[0];
+                var refLayer = results[1].layers[1];
                 t.deepEqual(layer.layout, refLayer.layout);
                 t.deepEqual(layer.type, refLayer.type);
                 t.deepEqual(layer.id, refLayer.ref);
@@ -333,7 +323,7 @@ test('Style#featuresAt', function(t) {
             style.featuresAt([256, 256], {}, function(err, results) {
                 t.error(err);
 
-                var layer = results[0].layer;
+                var layer = results[0].layers[0];
                 t.equal(layer.something, 'else');
 
                 t.end();