Abstract: To provide more accurate basic data for the genetic resources of Trionyx sinensis of Wuchang lake，and protect and utilize their germplasm resources，microsatellite marker technology was used to analyze the genetic diversity of T. sinensis from wild population of Wuchang lake and two breeding populations as experimental objects. The results showed that the average number of alleles（ Na）for the three populations were 11.5，9.1 and 7.9 respectively，average effective numbers of alleles（ Ne） were 6.3，3.7 and 3.1 respectively，average observed heterozygosity （Ho） were 0.5667，0.5222 and 0.4462 respectively，average expected heterozygosity（ He） were 0.6987，0.5953 and 0.5648 respectively and the average polymorphism information content（ PIC） were 0.6672， 0.5551 and 0.5303 respectively，the genetic diversity of Wuchang Lake population was higher，the Nei’s genetic distance and genetic differentiation showed that the germplasm resources preservation of Wuchang Lake population was better now.