Genetic diversity was investigated using assay of vertical slab ployacrylamide gel electrophoresis for the nine populations of Fenneropenaeus penicillatus. The results showed high levels of genetic diversity in each of the nine F. penicillatus populations. The mean number of alleles per locus ranged from 1.3333 to 1.6667, with a average of 1.4148. And the mean effective number of alleles per locus ranged from 1.1447 to 1.2094, with a average of 1.1664. The average of percentage of polymorphic loci was 26.67%, ranging from 13.33% to 40.00%. The average of observed heterozygosity was 0.1380, ranging from 0.1311 to 0.1511, and the average of expected heterozygosity was 0.0866, ranging from 0.0720 to 0.1023. The coefficient of gene differentiation among populations is low, indicating that only 2.09% of the total genetic diversity comes from inter-population, while the remaining 97.91% comes from intra-population differences. The genetic distance among populations is 0.0002¿0.0049 and gene flow among the populations is large. The results suggest that genetic structure is very similar among the nine F. penicillatus populations studied.