Abstract: EST-SSR was used to detect the hereditary difference in wild and cultured populations of the Betaphycus gelatinae,the result showed that nine individuals from each population were used of the 5 EST-SSR primers amplified,a total of 195 reproducible loci ranging from 250 to 2 500 bp were amplified from all the 18 individuals.The average percentages of polymorphic loci in wild and cultured populations were 74.29% and 70%.The intra-population genetic distance was 0.46 in wild population and 0.22 in cultured population.The cluster analysis showed that 18 individuals were clustered into two groups base on 0.49 of GS; wild populations were divided into 3 branches and cultured populations were divided into 2 branches base on 0.66; wild populations were divided into 5 branches and cultured populations were divided into 3 branches base on 0.73.The higher the value,the more branches the wild populations have.The research shows that genetic diversity of wild populations ampler than cultured.