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EST-derived SSR marker has been developed in many species,but few methods of high efficiency have been reported for the exploitation of EST-SSR markers.Thus,a high efficiency method for mining millions of redundant EST data is needed.A modified method for the EST-SSR development with high efficiency was established based on the redundant EST data of soybean in this study.The method achieved its function through classifying ESTs according to the same SSR motif and detected candidate loci with redundant sequences.In this study,a total of 80 polymorphic EST-SSR markers of soybean were developed,50 of them were exploited by this modified method which proved the higher speed and efficiency of this method.All the 80 polymorphic EST-SSRs were mapped on soybean physical map through in silico mapping and 15 markers were integrated on a genetic map constructed in previous study.A software named hpSSR (high polymorphic SSR) was programmed based on the concept of the up-built method for EST-SSR development.This method is not only pragmatic for EST-SSR exploitation in soybean,but also effective for the development of the marker in other species if the redundancy EST data is available.