Genetic diversity and differentiation were investigated using assay of vertical slab ployacrylamide gel electrophoresis for the nine populations of Marsupenaeus japonicus. The results showed high levels of genetic diversity in each of the nine M. japonicus populations. The mean number of alleles per locus ranged from 1.0000 to 1.0152, with a average of 1.0017, and the mean effective number of alleles per locus ranged from 1.1137 to 1.2012, with a average of 1.1463. the average of percentage of polymorphic loci was 18.18%, ranging from 13.64% to 22.73%, the average of observed heterozygosity was 0.0907, ranging from 0.0742 to 0.1121 and the average of expected heterozygosity was 0.0714, ranging from 0.0573 to 0.0930. The coefficient of gene differentiation among populations is low (0.0432), indicating that only 4.32% of the total genetic diversity comes from inter-population, while the remaining 95.68% comes from intra-population differences. The genetic distance among populations is 0.0002～0.0123 and gene flow among the populations is large (5.5406). The results suggest that genetic structure is very similar among the nine M. japonicus populations studied.