Using single-pair mating, 3 Nile tilapia families (N2 strain) were produced. Besides, consulting the second-generation linkage map of the tilapia genome, we used microsatellite primer to analyze genetic pleomorphism in the linkage group 1(LG1), LG3, LG14, LG15 and LG23. After detecting about 40 locus, we selected 6 locus (UNH995, GM354, UNH898, UNH168, UNH155 and UNH986) which were pleomorphism. Three (UNH995, GM354 and UNH898) of 6 locus could be used to distinguish 3 Nile tilapia families. Furthermore, we have kept a record of microsatellite locus information on website (Aquatic germplasm information network in Taiwan, http://agin.ph.tfrin.gov.tw/wfg/) for establishing genetic library of tilapia.