Abstract: Using high-throughput sequencing,we characterized 20 pairs of polymorphic microsatellite primers from Crassostrea sikamea genome, and we examined the markers in a wild population. A total of 330 alleles were found in 25 microsatellites.The observed number of alleles (N_a) ranged 6-39 in average of 16.500 0,and the effective number of alleles(N_e) ranged 1.352 9-33.361 7. The observed and expected heterozygosity values range 0.200 0-1.000 0 and 0.265 6-0.987 7, respectively.The Shannon Weiner index ranged 0.648 3-3.585 8 and Polymorphic information content (PIC) ranged 0.254 5-0.969 2. 16 microsatellite markers accord with Hardy-Weinberg equilibrium. Using these loci to analyze the genetic diversity of a cultured population, the average number of alleles was 10.25; the average number of N_e was 5.843 4. The observed heterozygosity (H_o) average was 0.639 1; the expected heterozygosity (H_e) average was 0.763 6; the Shannon-wiener index ( I ) average was 1.791 4; and the polymorphic information content (PIC) average was 0.720 7. It was found that the genetic diversity of C. sikamea cultured population was lower than that of the wild population, but it maintained a high-genetic diversity. The results of this study indicate that in the artificial breeding process of C. sikamea, the use of a large number of parents for breeding can effectively prevent the decline of genetic diversity of the cultured population, but artificial breeding also has a certain impact on the genetic diversity of the cultured population. The 20 loci were surveyed the cross-species proportions in C. angulate, C. gigas, C. hongkongensis, C. ariakensis, Saccostrea cucullata, Ostrea mordax and Hyotissa hyotis. Loci XB1-6, XB1-39, and XB1-45 can amplify the target band in 8 species, and the XB1-41 can only amplify the target band in C. sikamea.