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This paper discusses the development of a Web-based media annotation application named Synote, which addresses the important issue that while the whole of a multimedia resource on the Web can be easily bookmarked, searched, linked to and tagged, it is still difficult to search or associate notes or other resources with a certain part of a resource. Synote supports the creation of synchronized notes, bookmarks, tags, links, images and text captions. It is a freely available application that enables any user to make annotations in and search annotations to any fragment of a continuous multimedia resource in the most used browsers and operating systems. In the implementation, Synote categorized different media resources and synchronized them via time line. The presentation of synchronized resources makes full use of Web 2.0 AJAX technology to enrich interoperability for the user experience. Positive evaluation results about the performance, efficiency and effectiveness of Synote were returned when using it with students and teachers for a number of undergraduate courses.