Abstract: The products amplified by Random Amplified Polymorphism DNA(RAPD) techniques are always variable in different experiments. In order to establish a universal RAPD molecular marker system for grass carp genomic DNA polymorphism analysis,selected polymorphism RAPD loci should be checked by using different strains with distinct genetic backgrounds according to the law of Mendelian genetics. In this experiment, some polymorphic RAPD loci that could be employed as molecular markers for grass carp genomic DNA analysis have been examined by comparatively analyzing the genomes of theXiangjiang River grass carp group(Xiangjiang group) and a two-generation artificial induced meio-gynogenetic grass carp group(meio-gynogenetic-2 group). The Xiangjiang group can provide distinct genetic backgrounds samples andmay include all the genotype of grass carp,while the meiogynogenetic-2 group can provide clear genetic background samples. The different characterizations of the two groups can help identify the polymorphic RAPD loci in grass carp. Total 36 individuals of the Xiangjiang group and total 29 individuals of meiogynogenetic-2 group were examined with 10 polymorphism random primers in this experiment.With RAPD-PCR method, total 30 polymorphic loci have been identified in Xiangjiang group. In meiogynogenetic- 2 group, 17 of the polymorphic loci identified in Xiangjiang group were not detected in all the examined individuals. Only 13 of the 30 polymorphic loci in Xiangjiang group were identified in meio-gynogenetic-2 group.However only 7 of the 13 detected loci showed polymorphism, the other 6 lociwere identified in all the individuals in meio-gynogenetic-2 group and no polymorphism was observed. Because the meio-gynogenetic-2 individuals are highly purified during the gynogenesis and artificial selection for two generations, obviously, the 17 polymorphic loci that were undetected in meio-gynogenetic-2 group but in Xiangjiang group and the 6 polymorphic loci that detected in all the examined individuals of the meio-gynogenetic-2 group are the real polymorphic loci in grass carp.A chi-squared test was done on the 7 loci that show polymorphism to determine if the ratio of the detected and undetected individualswere consistent with the 1B1 expected ratio. The P values of the 7 polymorphic loci are from 0. 1936 to 0. 5775. This genetic statistical analysis indicated that the 7 polymorphic loci in Xiangjiang group and meio- gynogenetic-2 group are also consistent with the law of Mendelian genetics well. The 30 polymorphic RAPD loci, therefore, could be used as reliable molecular markers for the grass carp genomic DNA analysis. The observat ion that 17 polymorphic loci have been lost during the process of the two-generation artificial gynogenesis strongly suggested that protection of the diversity of natural grass carp resource and selection of homozygous traits with desired economic genotypes are both very important for grass carp breeding.