Abstract: The use and progress of molecular markers promotes development and innovation of aquaculture. In-depth research on the molecular level is a major innovation in aquatic industry. This article introduce the progress and change of microsatellite markers, the advantage of EST -SSR technology. The application of microsatellite markers in wild and domestic aquatic animal researches were presented, including genetic diversity, quantitative trait loci (QTL), fish breeding,population genetics structure and germplasm identification. Finally, the useful and prospect of mincrosatellite molecular marker techniques were presented.