Genetic variation between wild populations of Pinctada maxima from Sanya and Beihai was assessed by microsatellite DNA. The result showed that average number of alleles (A) was 10.50 and 9.67, and average number of effective alleles (Ne) was 7.01 and 6.33, respectively. The average observed heterozygosity (Ho) was 0.588 and 0.445, and the expected average heterozygosity (He) was 0859 and 0828, respectively. The average polymorphism information content (PIC) was 0.853 and 0.796, respectively. Hardy Weinberg equilibrium analysis revealed that these two populations showed some genetic disequilibria at the most loci except the loci of Pmx+022, Pmx16_41 and Pmx16_23 in Sanya population.