diff --git a/lib/core/utils/qsa.js b/lib/core/utils/qsa.js
index 1a6db08905..ac32c21ad7 100644
--- a/lib/core/utils/qsa.js
+++ b/lib/core/utils/qsa.js
@@ -29,7 +29,7 @@ function matchesPseudos (target, exp) {
 
 	if (!exp.pseudos || exp.pseudos.reduce((result, pseudo) => {
 		if (pseudo.name === 'not') {
-			return result && !matchExpressions([target], pseudo.expressions, false).length;
+			return result && !matchExpressions([target], pseudo.expressions, false, target.shadowId).length;
 		}
 		throw new Error('the pseudo selector ' + pseudo.name + ' has not yet been implemented');
 	}, true)) {
@@ -38,27 +38,6 @@ function matchesPseudos (target, exp) {
 	return false;
 }
 
-function matchSelector (targets, exp, recurse) {
-	var result = [];
-
-	targets = Array.isArray(targets) ? targets : [targets];
-	targets.forEach((target) => {
-		if (matchesTag(target.actualNode, exp) &&
-				matchesClasses(target.actualNode, exp) &&
-				matchesAttributes(target.actualNode, exp) &&
-				matchesId(target.actualNode, exp) &&
-				matchesPseudos(target, exp)) {
-			result.push(target);
-		}
-		if (recurse) {
-			result = result.concat(matchSelector(target.children.filter((child) => {
-				return !exp.id || child.shadowId === target.shadowId;
-			}), exp, recurse));
-		}
-	});
-	return result;
-}
-
 var escapeRegExp = (function(){
 	/*! Credit: XRegExp 0.6.1 (c) 2007-2008 Steven Levithan <http://stevenlevithan.com/regex/xregexp/> MIT License */
 	var from = /(?=[\-\[\]{}()*+?.\\\^$|,#\s])/g;
@@ -194,27 +173,80 @@ convertExpressions = function (expressions) {
 	});
 };
 
-matchExpressions = function  (domTree, expressions, recurse) {
-	return expressions.reduce((collected, exprArr) => {
-		var candidates = domTree;
-		exprArr.forEach((exp, index) => {
-			recurse = exp.combinator === '>' ? false : recurse;
-			if ([' ', '>'].includes(exp.combinator) === false) {
-				throw new Error('axe.utils.querySelectorAll does not support the combinator: ' + exp.combinator);
+function createLocalVariables (nodes, anyLevel, thisLevel, parentShadowId) {
+	let retVal = {
+		nodes: nodes.slice(),
+		anyLevel: anyLevel,
+		thisLevel: thisLevel,
+		parentShadowId: parentShadowId
+	};
+	retVal.nodes.reverse();
+	return retVal;
+}
+
+function matchesSelector (node, exp) {
+	return (matchesTag(node.actualNode, exp[0]) &&
+			matchesClasses(node.actualNode, exp[0]) &&
+			matchesAttributes(node.actualNode, exp[0]) &&
+			matchesId(node.actualNode, exp[0]) &&
+			matchesPseudos(node, exp[0])
+		);
+}
+
+matchExpressions = function  (domTree, expressions, recurse, parentShadowId, filter) {
+	//jshint maxstatements:34
+	//jshint maxcomplexity:15
+	let stack = [];
+	let nodes = Array.isArray(domTree) ? domTree : [domTree];
+	let currentLevel = createLocalVariables(nodes, expressions, [], parentShadowId);
+	let result = [];
+
+	while (currentLevel.nodes.length) {
+		let node = currentLevel.nodes.pop();
+		let childOnly = []; // we will add hierarchical '>' selectors here
+		let childAny = [];
+		let combined = currentLevel.anyLevel.slice().concat(currentLevel.thisLevel);
+		let added = false;
+		// see if node matches
+		for ( let i = 0; i < combined.length; i++) {
+			let exp = combined[i];
+			if (matchesSelector(node, exp) &&
+				(!exp[0].id || node.shadowId === currentLevel.parentShadowId)) {
+				if (exp.length === 1) {
+					if (!added && (!filter || filter(node))) {
+						result.push(node);
+						added = true;
+					}
+				} else {
+					let rest = exp.slice(1);
+					if ([' ', '>'].includes(rest[0].combinator) === false) {
+						throw new Error('axe.utils.querySelectorAll does not support the combinator: ' + exp[1].combinator);
+					}
+					if (rest[0].combinator === '>') {
+						// add the rest to the childOnly array
+						childOnly.push(rest);
+					} else {
+						// add the rest to the childAny array
+						childAny.push(rest);
+					}
+				}
 			}
-			candidates = candidates.reduce((result, node) => {
-				return result.concat(matchSelector(index ? node.children : node, exp, recurse));
-			}, []);
-		});
-
-		// Ensure elements aren't added multiple times
-		return candidates.reduce((collected, candidate) => {
-			if (collected.includes(candidate) === false) {
-				collected.push(candidate);
+			if (currentLevel.anyLevel.includes(exp) &&
+				(!exp[0].id || node.shadowId === currentLevel.parentShadowId)) {
+				childAny.push(exp);
 			}
-			return collected;
-		}, collected);
-	}, []);
+		}
+		// "recurse"
+		if (node.children && node.children.length && recurse) {
+			stack.push(currentLevel);
+			currentLevel = createLocalVariables(node.children, childAny, childOnly, node.shadowId);
+		}
+		// check for "return"
+		while (!currentLevel.nodes.length && stack.length) {
+			currentLevel = stack.pop();
+		}
+	}
+	return result;
 };
 
 /**
@@ -227,9 +259,26 @@ matchExpressions = function  (domTree, expressions, recurse) {
  * @return {NodeList} Elements matched by any of the selectors
  */
 axe.utils.querySelectorAll = function (domTree, selector) {
+	return axe.utils.querySelectorAllFilter(domTree, selector);
+};
+
+/**
+ * querySelectorAllFilter implements querySelectorAll on the virtual DOM with
+ * ability to filter the returned nodes using an optional supplied filter function
+ *
+ * @method querySelectorAll
+ * @memberof axe.utils
+ * @instance
+ * @param  {NodeList} domTree flattened tree collection to search
+ * @param  {String} selector String containing one or more CSS selectors separated by commas
+ * @param  {Function} filter function (optional)
+ * @return {NodeList} Elements matched by any of the selectors and filtered by the filter function
+ */
+
+axe.utils.querySelectorAllFilter = function (domTree, selector, filter) {
 	domTree = Array.isArray(domTree) ? domTree : [domTree];
 	var expressions = axe.utils.cssParser.parse(selector);
 	expressions = expressions.selectors ? expressions.selectors : [expressions];
 	expressions = convertExpressions(expressions);
-	return matchExpressions(domTree, expressions, true);
+	return matchExpressions(domTree, expressions, true, domTree[0].shadowId, filter);
 };
diff --git a/lib/core/utils/select.js b/lib/core/utils/select.js
index 029db974cf..a751df14ab 100644
--- a/lib/core/utils/select.js
+++ b/lib/core/utils/select.js
@@ -73,6 +73,22 @@ function pushNode(result, nodes, context) {
 	return result;
 }
 
+/**
+ * returns true if any of the nodes in the list is a parent of another node in the list
+ * @param {Array} the array of include nodes
+ * @return {Boolean}
+ */
+function hasOverlappingIncludes(includes) {
+	let list = includes.slice();
+	while (list.length > 1) {
+		let last = list.pop();
+		if (list[list.length - 1].actualNode.contains(last.actualNode)) {
+			return true;
+		}
+	}
+	return false;
+}
+
 /**
  * Selects elements which match `selector` that are included and excluded via the `Context` object
  * @param  {String} selector  CSS selector of the HTMLElements to select
@@ -83,6 +99,10 @@ axe.utils.select = function select(selector, context) {
 	'use strict';
 
 	var result = [], candidate;
+	if (!Array.isArray(context.include)) {
+		context.include = Array.from(context.include);
+	}
+	context.include.sort(axe.utils.nodeSorter); // ensure that the order of the include nodes is document order
 	for (var i = 0, l = context.include.length; i < l; i++) {
 		candidate = context.include[i];
 		if (candidate.actualNode.nodeType === candidate.actualNode.ELEMENT_NODE &&
@@ -91,6 +111,8 @@ axe.utils.select = function select(selector, context) {
 		}
 		result = pushNode(result, axe.utils.querySelectorAll(candidate, selector), context);
 	}
-
-	return result.sort(axe.utils.nodeSorter);
+	if (context.include.length > 1 && hasOverlappingIncludes(context.include)) {
+		result.sort(axe.utils.nodeSorter);
+	}
+	return result;
 };
diff --git a/test/core/utils/qsa.js b/test/core/utils/qsa.js
index d9483cc267..18109b25b9 100644
--- a/test/core/utils/qsa.js
+++ b/test/core/utils/qsa.js
@@ -109,6 +109,10 @@ describe('axe.utils.querySelectorAll', function () {
 		var result = axe.utils.querySelectorAll(dom, '#one');
 		assert.equal(result.length, 1);
 	});
+	it('should find nodes using id, but not in shadow DOM', function () {
+		var result = axe.utils.querySelectorAll(dom[0].children[0], '#one');
+		assert.equal(result.length, 1);
+	});
 	it('should find nodes using id, within a shadow DOM', function () {
 		var result = axe.utils.querySelectorAll(dom[0].children[0].children[2], '#one');
 		assert.equal(result.length, 1);
@@ -182,4 +186,10 @@ describe('axe.utils.querySelectorAll', function () {
 		assert.isBelow(divOnes.length, divs.length + ones.length,
 			'Elements matching both parts of a selector should not be included twice');
 	});
+	it('should return nodes sorted by document position', function () {
+		var result = axe.utils.querySelectorAll(dom, 'ul, #one');
+		assert.equal(result[0].actualNode.nodeName, 'UL');
+		assert.equal(result[1].actualNode.nodeName, 'DIV');
+		assert.equal(result[2].actualNode.nodeName, 'UL');
+	});
 });
diff --git a/test/core/utils/select.js b/test/core/utils/select.js
index 48bff29677..2ac60392a6 100644
--- a/test/core/utils/select.js
+++ b/test/core/utils/select.js
@@ -136,6 +136,18 @@ describe('axe.utils.select', function () {
 
 	});
 
+	it('should sort by DOM order on overlapping elements', function () {
+		fixture.innerHTML = '<div id="zero"><div id="one"><div id="target1" class="bananas"></div></div>' +
+			'<div id="two"><div id="target2" class="bananas"></div></div></div>';
+
+		var result = axe.utils.select('.bananas', { include: [axe.utils.getFlattenedTree($id('one'))[0],
+			axe.utils.getFlattenedTree($id('zero'))[0]] });
+
+		assert.deepEqual(result.map(function (n) { return n.actualNode; }),
+			[$id('target1'), $id('target1'), $id('target2')]);
+		assert.equal(result.length, 3);
+
+	});
 
 
 });
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