Transgenic organism contains modified genes, including genes from other species. The escape or introduction of transgenic organisms into a natural environment poses a major ecological concern. Purdue University researchers Willian and Richard have found that introduction of a transgenic fish to the wild could damage native populations, even to the point of extinction. Such environmental risk should be evaluated before releasing every transgenic animal into a wild environment. Here we report a risk assessment of releasing the transgenic carp bearing the brevoort growth hormone gene into a natural population using a panel of 265 RAPD markers and 35 microsatellite markers. This risk assessment was based on detecting population genetic background changes and comparing these changes with the hybrid carps that may also present a latent threat to native wildlife. In this study, we have chosen seven experimental groups that are Heilong River carps inside Harbin section, Heilong River carps inside Fuyuan section, Heilong River carps inside Songhua River, two fry groups that one or ten percent transgenic carps were mixed with common carps respectively, and two equivalent fry groups as controls. All groups were bred under similar environment to minimize other variables. The transgenic carps were produced by inserting a gene construct of salmon growth hormone driven under the salmon growth hormone promoter into genomes of common carps. Heilong River carps inside Harbin section represented a population polluted by hybrid carps. The group of Heilong River carps inside Fuyuan section served as a natural group as it is away from cities and artificial nurseries, and grows mostly in the wild. Through genome wide scanning of every experimental group and statistical analysis, we found the frequency of correlation between transgene and heterozygosity is 0.02. P value of heterozygosity of Heilongjiang carps inside Harbin is 0.08 which is significent. Based on these results, we concluded that the exogene pollution in both groups in which one or ten percent transgenic carps were mixed is significantly lower than that of the hybrid carps to the natural carps. These data suggested that the ecological risk of growth-homone transgenic carps is less than the hybrid carps. The transgenic carps could not cause serious gene pollution to the natural carps unless a large number of transgenic carps escaped or released to the natural environment. Although we must try our best not to release any non-natural organism especially transgenic organism to the wild, it is necessary to analyze the risk of accidental releases. In this study, our data suggested that the hazard of transgenic organisms to wildlife is not greater than exotic and hybrid species. The natural world seemed not as rigid as we had thought, and complex genetic resources could neutralize the influence of a transgene.