Abstract: Genetic diversity and differentiation among three stocks of selected GIFT strains of Oreochromis niloticus was analyzed using microsatellite DNA and AFLP markers. Nine microsatellite loci and four primer pairs of AFLP revealed consistent results. Microsatellite data showed that Qingdao GIFT stock had the highest mean number of alleles (4.8), mean observed heterozygosity (0.528) and mean PIC (0.605), whereas Hainan GIFT the lowest. AFLP analysis demonstrated that Qingdao GIFT had the highest proportion of polymorphic loci (48.4%) and gene diversity within populations (0.245), whereas Hainan GIFT the lowest. These observations indicated that Qingdao GIFT has the highest genetic diversity, whereas Hainan GIFT the lowest. Genetic differentiation among the three GIFT strains was significant as revealed by microsatellite (FST=0.07~0.11, P0.01) and AFLP FST =0.24~0.29, P0.01). AMOVA indicated that the majority of genetic variation (91.26% by microsatellite analysis and 67.6% by AFLP) was attributed to difference of individuals within stocks, suggesting that GIFT strains of O.niloticus has some potential for further selective breeding.