Abstract: With 10 polymorphic microsatellite markers, we studied the genetic variation in silver-lip pearl oyster (Pinctada maxima) populations of 3 year-classes (2007, 2009, 2010)from Sanya, Hainan, China.For each population we collected 30 samples, and 60 alleles were amplified among 10 loci using PCR, each locus including 2~8 alleles. Three populations lost 1, 2 and 4 rare alleles, respectively. The average expected heterozygosity, PIC value and Shannon′s information index all decrease. Moreover, there is an overall deficit of heterozygotes for the populations. Eighteen out of 30 loci are deviated from Hardy-Weinberg equilibrium. The average pairwise inbreeding coefficient F_IS ranges from 0.227 3 to 0.260 1, and the pairwise F_ST value ranges from 0.020 4 to 0.046 2, indicating a significant genetic differentiation (P < 0.01).This study suggests that the genetic diversity and the degree of inbreeding for the populations of 3 year-classes decrease from generation to generation, and their genetic structures differ from one another significantly. Thus, it is necessary to avoid inbreeding and to maintain the genetic diversity during artificial reproduction.