Abstract：17 distinguished loci were screened out of 77 microsatellite to check the genomic DNA of three varieties of, including differential locus of O.aureus UNH636, UNH117, UNH172, UNH738, UNH878, UNH896, O. niloticus UNH913, UNH907, UNH222, UNH980, UNH880 and O. mossambicu UNH876, UNH899, UNH853, UNH932, UNH933, UNH773. Anyone of 17 loci amplified particular bands of one strain of tilapia. So these loci can distinguish one tilapia from the other. The genetic structure and the phylogenetic relationships of three tilapias were analysis by using this 17 microsatellite loci, there were totally 142 alleles of these microsatellite loci, and the average number of alleles was 8.35. Additionally, a clustering analysis was made based on the result of the Popgen32 software package and phylogenetic trees were constructed by MEGA4 using UPGMA method. The results showed that, the mean value of observed heterozygosity of O. aureus, O. niloticus and O. mossambicu was 0.0941, 0.5490, 0.2588, the mean value of expected heterozygosity was 0.1089, 0.7230, 0.2608, and the polymorphism information content (PIC) was 0.1089, 0.7230 and 0.2608 respectively. It indicated that, the genetic diversity of O. niloticus was highest and O.aureus was lowest. The phylogenetic tree shows that the genetic relation between O.aureus and O. mossambicu is closer than their relationship with O. niloticus, which was similar to others reports.
