Abstract: The genetic diversity and phylogenetic relationships among five breed varieties of red tilapia (GD, ZZ, FL, MY, ML) were analyzed by using 22 pairs of microsatellite primers. Stable and clear amplification bands could be amplified in 16 pairs of primers from 5 red tilapia populations by PCR. 16 pairs of microsatellite DNA primers which were selected and proved to amplify successfully on red tilapia by pre-experiment were used. The genetic diversity index of 5 red tilapia populations showed that:a total of 146 alleles were detected from 16 microsatellite markers. The ave-rage allele numbers ranged from 6.5625 to 8.5625 and the average effective allele numbers ranged from 4.1495 to 6.1330, respectively. The expected value of average heterozygosities ranged from 0.7491 to 0.8247 and the average polymorphism information contents were ranged from 0.6939 to 0.7840, respectively. Chi-square tests showed that most loci in the 5 red tilapia groups deviated from Hardy-Weinberg equilibrium. The largest genetic distance (0.4827) and the lowest genetic similarity index (0.6171) were found between red tilapia (GD) and red tilapia (ZZ), which suggested a farthest phylogenetic relationship between these two groups. On the other hand, the highest genetic similarity index (0.9069) and the lowest genetic distance (0.0977) were found between red tilapia (FL) and red tilapia (ML), which indicated a closer phylogenetic relationship between these two populations. Phylogenetic relationship of the five populations was analyzed by using UPGMA methods and the results showed that red tilapia (FL) and red tilapia (ML) populations were clustered in the first group, the red tilapia (ZZ) in the second group, the red tilapia (MY) in the third group, while the red tilapia (GD) was in a separate group. Such results indicated that the five red tilapia populations maintained relatively high genetic diversity and still had potential for breeding.