Using a new hybird [NEW GIFT Nile tilapia (Oreochromis niloticus)♀× blue tilapia(O. aureaus)♂, short term JA] and closed hybrid (common Nile tilapia ♀× blue tilapia♂, short term AN) as well as their parents(GIFT Nile tilapia, short term XJ; common Nile tilapia, short term NL; blue tilapia, short term AL) as study materials, their genetic variations were studied by RAPD and SSR technologies. By RAPD:①Percentage of polymophism loci（P）-JA（20.4%）>XJ（18.5%），but < AL（21.4%）I_p)-JA（0.9086） AL（0.8895）>NL（0.8588）>AN（0.8069）；③Shannon diveristy index(H_o)-JA(0.1326)>XJ（0.1103），but < AL（0.1514）I_pop)-JA-AN (0.9444)< JA-NL(0.9496) JA-AL（0.9383）.By SSR:①Average effective numbers of alleles（N_e）-JA(2.43)>XJ(2.31)>NL（1.94）>AL（1.18），but < AN（2.82）；②Average heterozygosity（H）JA (0.700) > NL（0.570）>AL（0.497）>XJ(0.398)，but< AN (0.816)；③ polymorphism imformation content（PIC）-JA（0.661）>NL（0.568）>AL（0.513）>XJ（0.420），but < AN（0.692）；④The Nj and UPGMA tree based on genetic distance showed that, AL goes to one branch seperately, JA etc. 4 genotypes run togather into a branch. In general, the information by RAPD and SSR all revealed that, the hybrid, never mind JA or AN, all closed to their mother side, which is coincident with the our previous study results from morphology and growth.