We evaluated the genetic diversity of three wild populations [Zhanjiang (ZJ), Beihai (BH), Jingpu (JP)] of in the Beibu Gulf using 20 microsatellite DNA loci. We calculated the allele numbers, effective allele numbers, expected heterozygosity, observed heterozygosity and Hardy-Weinberg equilibrium. Three loci were monomorphic and 17 loci were polymorphic. Five loci in each population deviated significantly from Hardy-Weinberg equilibrium. The locus exhibited significant deviation from Hardy-Weinberg equilibrium in all 3 populations. Though diversity was higher in JP than in BH and ZJ, analysis across the stocks and loci revealed a low level of divergence. We constructed NJ and UPGMA clustering trees based on genetic distance. The populations from nearby geographical locations were clustered together in both trees.