On April 2009, a base population (F0) of the Fujian oyster, , was selectively bred from the Fujiang and Guangdong local populations. A successive six-generation selection for golden shell and body weight was carried out to produce "Golden oyster 1#" (F6). In this study, eight microsatellite markers were analyzed in the base population, selected line F6, and wild populations of . The number of alleles per locus ranged from 7 to 24. The average number of alleles and average allelic richness of the three populations at all loci had ranges of 10.3-17.6 and 9.8-16.8, respectively. Expected heterozygosity and observed heterozygosity were 0.655-0.662 and 0.788-0.872, respectively. In the Hardy-Weinberg equilibrium test, for the three populations and eight microsatellites, segregation distortion was significant for 12 of the 18 groups. The inbreeding coefficient (F_st values were 0.0224-0.1627, with an average of 0.0767, indicating that there is a low level of inbreeding within populations and a high level of differentiation. Our results suggested that successive artificial breeding has a certain influence on genetic variation; however, there remains high genetic variability in the mass selection lines.