Gene flow is an important ecological and genetic process, and the fitness conferred by the insertion of a foreign gene could be important in ecology after it becomes introgressed into the wild genetic background of organisms, which is the determinative factor for the fate of GMOs or foreign genes in natural ecosystem and for the competition with native species. Trophic interrelation fulfilled by food chains is the most important correlation between species in ecosystem and could be affected by the modified genotypes after the introduction of GMOs. The technology enabling the precise manipulation of genotype is a great opportunity for the study of ecological genetics in an unknown way prior to the biotechnology era. Especially interesting is the impact of genes on ecosystem function when GMOs are released into environment. A variety of ecological terminology has been frequently used in assessment of ecological risks related to the release of GMOs in environment, e.g. gene flow, fitness, interspecific competition and food chain. The value of GMOs in ecological research is illustrated through several examples in biosafety assessment related to those terms here. It is proposed that ecologists should pay attention to the study of gene function in ecosystem and take the opportunity to enrich ecological theory with the release of GMOs.