diff --git a/src/ui/filter.js b/src/ui/filter.js
index 5e37c4513..29a8bf2ab 100644
--- a/src/ui/filter.js
+++ b/src/ui/filter.js
@@ -160,10 +160,14 @@ Filter.prototype.updateFilter = function (filter) {
         return;
     }
 
-    var annotations = this.highlights.map(function () {
-        return $(this).data('annotation');
-    });
-    annotations = $.makeArray(annotations);
+    var annotations = (function (highlights) {
+        var annotationsById = {};
+        highlights.each(function () {
+            var a = $(this).data('annotation');
+            annotationsById[a._local.id] = a;
+        });
+        return $.map(annotationsById, function(a) { return a; });
+    }(this.highlights));
 
     for (var i = 0, len = annotations.length; i < len; i++) {
         var annotation = annotations[i],
diff --git a/src/ui/highlighter.js b/src/ui/highlighter.js
index a4ebb5ce5..bc1b05a42 100644
--- a/src/ui/highlighter.js
+++ b/src/ui/highlighter.js
@@ -119,6 +119,15 @@ Highlighter.prototype.drawAll = function (annotations) {
     return p;
 };
 
+// local unique IDs for annotations, used to deduplicate when recovering them
+// from highlights.
+var id = (function () {
+    var counter = 0;
+    return function() {
+        return '_local_id_' + (++counter);
+    }
+}());
+
 // Public: Draw highlights for the annotation.
 //
 // annotation - An annotation Object for which to draw highlights.
@@ -140,10 +149,15 @@ Highlighter.prototype.draw = function (annotation) {
         annotation._local = {};
     }
     var hasHighlights = (typeof annotation._local.highlights !== 'undefined' &&
-                         annotation._local.highlights === null);
+                         annotation._local.highlights !== null);
     if (!hasHighlights) {
         annotation._local.highlights = [];
     }
+    var hasLocalId = (typeof annotation._local.id !== 'undefined' &&
+                      annotation._local.id === null);
+    if (!hasLocalId) {
+        annotation._local.id = id();
+    }
 
     for (var j = 0, jlen = normedRanges.length; j < jlen; j++) {
         var normed = normedRanges[j];
diff --git a/test/spec/ui/filter_spec.js b/test/spec/ui/filter_spec.js
index ad49a28bb..79d3f2c4f 100644
--- a/test/spec/ui/filter_spec.js
+++ b/test/spec/ui/filter_spec.js
@@ -124,15 +124,27 @@ describe('ui.filter.Filter', function () {
                 }
             };
             annotations = [{text: 'cat'}, {text: 'dog'}, {text: 'car'}];
+            $.each(annotations, function(i, annotation) {
+                this._local = {id: this.text};
+                for (var j = 0; j < annotation.text.length; j++) {
+                    var ch = annotation.text[j]
+                    $('<span class="annotator-hl">')
+                        .text(ch)
+                        .data('annotation', annotation)
+                        .appendTo(element);
+                }
+            });
             plugin.filters = {'text': testFilter};
-            plugin.highlights = {
-                map: function () { return annotations; }
-            };
+            plugin.highlights = $(element).find('.annotator-hl');
             sandbox.stub(plugin, 'updateHighlights');
             sandbox.stub(plugin, 'resetHighlights');
             sandbox.stub(plugin, 'filterHighlights');
         });
 
+        afterEach(function () {
+            $(element).empty();
+        });
+
         it("should call Filter#updateHighlights()", function () {
             plugin.updateFilter(testFilter);
             assert(plugin.updateHighlights.calledOnce);