s/highlight/highlighted/ for the search word highlighting class: "highlight" is already used by pygments.

sphinx/themes/agogo/static/agogo.css_t

@@ -118,6 +118,10 @@ p.admonition-title {
   font-weight: bold;
 }
 
+dt:target, .highlighted {
+  background-color: #fbe54e;
+}
+
 /* Header */
 
 div.header {

sphinx/themes/basic/static/basic.css

@@ -316,7 +316,7 @@ dd {
     margin-left: 30px;
 }
 
-dt:target, .highlight {
+dt:target, .highlighted {
     background-color: #fbe54e;
 }
 

sphinx/themes/basic/static/doctools.js

@@ -182,7 +182,7 @@ var Documentation = {
       var body = $('div.body');
       window.setTimeout(function() {
         $.each(terms, function() {
-          body.highlightText(this.toLowerCase(), 'highlight');
+          body.highlightText(this.toLowerCase(), 'highlighted');
         });
       }, 10);
       $('<li class="highlight-link"><a href="javascript:Documentation.' +
@@ -214,7 +214,7 @@ var Documentation = {
    */
   hideSearchWords : function() {
     $('.sidebar .this-page-menu li.highlight-link').fadeOut(300);
-    $('span.highlight').removeClass('highlight');
+    $('span.highlighted').removeClass('highlighted');
   },
 
   /**

sphinx/themes/basic/static/searchtools.js

@@ -31,7 +31,7 @@ jQuery.makeSearchSummary = function(text, keywords, hlwords) {
   ((start + 240 - text.length) ? '...' : '');
   var rv = $('<div class="context"></div>').text(excerpt);
   $.each(hlwords, function() {
-    rv = rv.highlightText(this, 'highlight');
+    rv = rv.highlightText(this, 'highlighted');
   });
   return rv;
 }

sphinx/themes/epub/static/epub.css

@@ -298,7 +298,7 @@ dd {
     margin-left: 30px;
 }
 
-dt:target, .highlight {
+dt:target, .highlighted {
     background-color: #ddd;
 }