The Japanese scallop(Patinopecten yesoensis) was introduced from Japan to Dalian in the 1980s. It has been cultured on large scale in this area. In this study genetic diversity of 5 cultured and natural populations of Japanese scallop were investigated by microsatellites. The 5 populations were the population in Zhangzidao island (CC), the natural population in north area of the Yellow Sea (HQ), Japanese cultured population (JX), Russian population (RX) and albino population collected in Dachangshan island (ZB). HQ is a natural population which has been collected in north area of Yellow Sea in 2005. A specific genetic marker was found in this population. Thirty individuals from each population were analyzed. Amplifications were performed in a PCR reactor with 8 microsatellite loci, tested by agarose gel eletrophoresis and analyzed by gel analysis software. In this study 45 alleles were obtained. The number of alleles of each locus ranged from 3 to 9, and allele size ranged from 100 to 340bp. The mean number of effective alleles (a_e) was 3.1535 and the number of genotypes ranged from 3 to 21 in each locus. PIC (Polymorphism Information Content) per locus ranged from 0.0322 to 05944. The average observed heterozygosity (H_o) for the five populations was 0.3292, 0.3048, 0.3167, 0.2708 and 03042, respectively. The average expected heterozygosity (H_e) for the 5 populations was 0.4595, 0.4002, 0.3838, 03620 and 0.3885, respectively. The difference in genetic diversity among the 5 populations is not significant. According to their genetic similarity (I) and genetic distance (D), we found that the genetic distance between CC and HQ was the least, followed by that of JX and RX. The distance between ZB to JX and RX were both closer than those of CC and HQ. The P value test of Hardy-Weinberg equilibrium showed that the populations departed from Hardy-Weinberg equilibrium in some loci. All 5 populations showed the absence of heterozygosity. The results of the F-test suggested high genetic differentiations among the 5 populations, and mainly due to individual difference.