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 (Ho) was 0.144 4～0.488 9. The expected heterozygosity (He) 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 Ho (0.129 2～0.466 7), average He (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. Neis genetic distance was used to construct the dendrogramby 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.