Manila clam is widely distributed and cultured along the coasts of China. To assess genetic variation in selected strains cultured in China, four selected strains or populations, zebra (Z), white (W), orange (O), and white zebra (WZ), along with one wild population from Lvshun were analyzed with 10 microsatellite loci. The observed heterozygosity ranged from 0.335–0.538 across populations. The highest expected heterozygosity value was detected in the Z strain (0.716), whereas the lowest value was found in the WZ strain (0.578). F_ST revealed significant differentiation between all pairs of populations. The differentiation between the W strain and the O strain is the lowest (F_ST = 0.086). whereas the differentiation between Z and WZ strains was the highest (F_ST = 0.337). There was no significant reduction in heterozygosity in all four selected strains; however, the number of alleles per locus was considerably lower in the selected strains than in the wild population. These results provide valuable genetic information for the preservation, management, and further selective breeding of the Manila clam.