Abstract: Genetic diversity and phylogenetic relationships among four breed varieties of Oreochromis aureus (83), O. au-reus (02), O. aureus (05) and red O. aureus were studied using microsatellite analysis technology. 19 pairs of microsatel-lite DNA primers of Oreochromis niloticu registered in GenBank which were selected and proved to amplify successfully on Oreochromis aureus by pre-experiment were used. The PCR reaction condition especially concentration of Mg2+and annealing temperature were adjusted for each pair of primers. Amplified PCR products were electrophoresed in PAGE and stained according to the silver stain procedures and then imagined by Alphalmager. A total of 82 alleles were obtained from the four populations. The number of alleles for each locus ranged from 2-8, and the average alleles was 4.3 each locus, Average observed heterozygosity and average expected heterozygosity were calculated by POPGENE3.2 software. The results showed that the observed value of average heterozy-gosity of the four O. aureus populations ranged from 0.154 to 0.391. The expected value of average heterozygosity ranged from 0.181 to 0.428, and the average polymorphism information contents ranged from 0.1513 to 0.3882, respectively. The lowest genetic diversity level was found in the O. aureus (02). The highest genetic similarity index (0.9422) and the lowest genetic distance (0.0596) were found between O. aureus (05) and O. aureus (83), which indicated a closer phy-logenetic relationship between these two populations. On the other hand, the lowest genetic similarity index (0.6977) and the highest genetic distance (0.3599) existed between O. aureus (83) and red O. aureus, which suggested a farthest phy-logenetic relationship between these two populations. The evaluation results of the genetic deviation index D revealed that there were loci departed from Hardy-Weinberg equilibrium in all the four O. aureus populations. Results of null allele anal-ysis by MicroChecker showed that there were loci showing evidences for null alleles in the populations except red O. aureus population, including one locus for O. aureus (83), two for O. aureus (02) and seven for O. aureus (05). Such results suggested that locus with evidence for null alleles in the populations except red O. aureus might be one of the reasons cau-sing deviation of Hardy-Weinberg equilibrium. Phylogenetie relationship of the four populations was analyzed by using UPGMA methods based on their genetic distances and the results showed that O. aureus (83) and O. aureus (05) popula-tions were clustered in the first group, the O. aureus (02) in the second group, while the red O. aureus was in a separate group.