In this study, meiosis gynogenesis was induced in Erythroculter ilishaeformis Bleeker using heterologous sperm, and cold-shock was performed to diploidize the female chromosome. The genomes of three groups of E. ilishaeformis, namely the Tai Lake group (control group), the first generation artificially induced meiosis gynogenetic group (meio-G1) and the second generation artificially induced meiosis gynogenetic group (meio-G2) were comparatively analyzed by simple sequence repeats(SSR)and random amplified polymorphic DNA (RAPD).The results of SSR indicated that the numbers of alleles among 12 loci were 38, 16 and 47 respectively, and the average numbers of alleles were 3.166 7, 1.333 3 and 3.916 7 respectively. The average values of observed heterozygosity in the three groups were 0.430 6, 0.333 3 and 0.675 0, and the average homozygosity were 0.569 4, 0.666 7 and 0.325 0. The average similarity indices among individuals within meio-G2 and control group were 1.000 0 and 0.571 9, which were higher than those within the meio-G1 group (0.543 0). The cluster results showed that meio-G1 and control groups cluster together firstly and the meio-G2 group clusters another branch independently. The results of RAPD showed the examined numbers of loci among 14 primers in the three groups were 74, 61 and 64, and the percent of polymorphic loci were 63.51%, 0 and 51.56% accordingly. The genetic similarities calculated according Nei's index were 1 for meio-G2 and 0.849 0 for control group, which were slightly higher than that in meio-G1 (0.801 8). The results of SSR and RAPD markers both indicated that the homozygosity and genetic similarity among individuals in meio-G2 were higher than those in meio-G1 and control group, and the genotypes of all the analyzed individuals in meio-G2 were the same. The meio-G2 family cultured in our study may be a good material in further selective breeding research.