The Manila clam, , which is widely distributed along the coasts of China, is an economically important marine bivalve species in China's aquaculture industry. The world production of this species was 3.6 million metric tons in 2010. As a country, China accounts for the largest proportion (~90%) of the total global production of Manila clams, producing about 3.0 million metric tons annually. This species includes several pedigree lines, such as White, Zebra, Liangdao Red, and Marine Red that are distributed in the coastal areas in North China. Microsatellite markers are a powerful tool because of their high level of polymorphism, stability, and co-dominance. As a result, they are used widely in studies of genetic diversity and population differentiation. In this study, 10 microsatellite markers were analyzed in three selected lines and one wild population of . The number of alleles per locus ranged from 3 to 12, and allelic richness range was 3.0-10.7. Among all SSR loci, the mean number of alleles breeding populations of white zebra strain was 4.4. Allelic richness was lowest in the breeding white clam population (4.267). The average number of alleles and allelic richness was highest in the wild population from Longwangtang (5.100 and 5.278, respectively). There was no difference in average allelic richness among all groups (Kruskal-Wallis test, d_{=0.412). Expected heterozygosity ranged from 0.307 to 0.757, and observed heterozygosity ranged from 0.208 to 0.583. The 77.5% inbreeding coefficient () was positive, indicating that there is a certain level of inbreeding within populations, resulting in varying degrees of loss of heterozygosity. The R. philippinarum were between 0.05 and 0.15, indicating a moderate level of differentiation. The values for comparisons between the Longwangtang population and the three shell colored lines were 0.15-0.25, indicating a greater level of differentiation. Our results suggest that genetic variation has not been significantly affected by mass selection and there remains high genetic variability in the mass selection lines, suggesting that there is still potential for increased gains in future selective breeding programs.}