Abstract: We studied the genetic diversity of breeding family of Pinctada fucata. Six microsatellite markers were chosen for genetic analysis of 360 individuals of nine families. A total of 32 alleles were detected and the number of allele at each locus was 3~8. The effective allele was 1.758 7~3.586 5. The observed heterozygosity (H_o) was 0.144 4~0.488 9. The expected heterozygosity (H_e) was 0.432 0~0.722 2 and the Shannon index was 0.691 9~1.507 4. Monomorphism loci were found in each family. The average H_o (0.129 2~0.466 7), average H_e (0.155 0~0.439 6) and Shannon index (0.248 5~0.712 2) were detected in family population. Nineteen loci (35.19%) were deviated from Hardy-Weinberg equilibrium test significantly. The genetic distance was 0.109 0~1.137 2 and the genetic identify index was 0.320 7~0.896 8. L₄B₄6 was the furthest with L₄B₄8 and the nearest with D₃D₃13 in terms of genetic distance. Nei′s genetic distance was used to construct the dendrogram by using the unweighted pair group method with arithmetic (UPGMA). Nine families were divided into three clusters: family L₄B₄8 clustered alone and layed outside, while three families (B₄D₄26, B₄D₄27 and D₄B₄45) clustered together, and the other families clustered into one clade. The study provides references for construction of next generation of nuclear populations in P. fucata selective breeding.