Selective breeding on growth character and disease2resistant trait of shrimp Fenneropenaeus chinensis has been conducted since 1997, and six successively bred stocks were produced between 1997 and 2002 at breeding base of the Yellow Sea Fisheries Research Institute, Shandong Province, China. Challenge Test has shown their better growth rate and disease2resistant performance than controlled shrimp. Samples of CP1 and CP6 were randomly collected. Tail muscle tissue from shrimp of mostly adults and sub2 adults was collected. Total DNA was extracted from tail muscle. DNA quality controls were performed using agarose gel electrophoresis and only samples with good DNA quality were used for microsatellite analysis. Microsatellite technique was used to investigate the genetic variation between the cultured populations (CP1 and CP6) of F . chinensis. Ten microsatellite primers were designed according to small2size fractionated genomic libraries of F. chinensis. Optimal results were obtained by optimizing quantity of reagents and reaction conditions. Under the optimal conditions, PCR was performed for analyzing the genetic diversity of the two selected populations. PCR products were electrophoresed through 8% polyacrylamide gels. Samples were heated to 95 e for 5 min before being loaded onto the polyacrylamide gels. The gels then were silver2stained. All samples were run next to a known sequence in order to determine size. To avoid inaccuracy in scoring due to differences in gels, a control DNA sample was included in each set of samples for each gel. To analyze the variation in microsatellite loci in the two populations, number of alleles per locus ( na ) , Polymorphism Information Content ( PIC) , number of genotypes per locus ( G ) effective number of alleles (Ae ) , observed heterozygosity (Ho) and expected heterozygosity (He) were estimated for each population at each locus. Allele frequencies for each population at each locus were calculated based on the number of alleles provided by the computer software TFPGA. A total of 74 different alleles were found over all ten loci. The total number of alleles per locus ranged from 3 to 13. In the two populations, the effective number of alleles was lower than the observed number. PIC per locus ranged from 0. 5567 to 0. 8877. The average heterozygosity of the first and sixth selected generation was 0. 6400 and 0. 6300, respectively. To access departures from HWE, P2 values of genotypic frequencies were calculated. Furthermore, five cases of observed heterozygosity excess ( Fis< 0 ) were observed in the two populations. Shannon genetic diversity index revealed that the average variation level of the two populations was 1. 7742, and the variation level of them was 1. 6830 and 1. 7382, respectively. Partitioning of the genetic variation revealed that 96. 415% is distributed within populations and 3. 585% among populations. Nei. s genetic identity and genetic distance between the two populations were 0. 9187 and 0. 0848, respectively. In summary, data showed low genetic diversity of F. chinensis and difference over the levels of genetic variation between the two populations. There was great potential of selective breeding for the sixth generation.