The genetic structure and variations of the cultured stock and artificial meiogynogenetic population of half-smooth tongue sole Cynoglossus semilaevis were analyzed by using twenty-four microsatellite markers. The results showed that the average numbers of alleles and average effective alleles were 7.0 and 4.8, and 3.935 and 2.411 in the cultured stock and the artificial gynogenetic population, respectively. The mean observed heterozygosity (HO) were 0.713 5 and 0.586 5, respectively. The results indicate that the genetic diversity of the cultured group was much higher than that of the gynogenetic population. Thirteen loci deviated significantly from Hardy-Weinberg equilibrium (HWE) in the gynogenetic population, while one loci deviated from HWE in the cultured group. The coefficient of gene differentiation (GST) was 0.131 0, and the genetic distance was 0.420 0 between the two populations, indicating for a significant genetic differentiation between the two populations.