Tilapia is one of the most extensively cultured species in aquaculture with great economic importance, and has been introduced to nearly 100 countries in the world. China is the biggest country in tilapia production, accounting for about 55% of the total production in the world. In which, Nile tilapia () has played an important role in developing tilapia industry. Since 1978, Nile tilapia first introduced to China, it has been multiply introduced from different countries or areas for several times. Consequently a number of domesticated strains or populations have been established and developed with different selective pressures and divergent genetic characteristics in China. This gives us a chance to combine multiple germplasm resources in breeding practices of tilapia. However, the genetic evaluation and investigation of these domesticated populations of Nile tilapia in China have been relatively poorly conducted. In this study, genetic diversity and genetic relationships of the eight domesticated populations of Nile tilapia in China were examined using partial mitochondrial control region (D-loop) sequence, including the Egypt (EGY), Gilada (GLD), American (USA), Luye (LY), Genomar (GNM), Baolu (BL), Guangdong (GD) and New GIFT (NGF) populations. The results showed that only 15 haplotypes were defined in the 237 analyzed individuals, in which, BL1 haplotype was shared by the five populations (BL, EGY, GLD, GNM, LY), but no one shared haplotype was found for all the populations. The Number of variable sites (), haplotype diversity () and 4 to 83, 0.50 to 37.26, 0.190 8 to 0.802 3 and0.000 8 to 0.056 9, respectively. The genetic diversity in the LY was the lowest in the eight populations analyzed. The results of analysis of molecular variance (AMOVA) indicated significant genetic divergence (<0.01) among the populations. The cluster analysis based on Kimura two-parameter model exhibited the two clusters among them, one cluster included the three populations of BL, GD and NGF, and another cluster consisted of the five populations of EGY, LY, GNM, GLD and USA. However, it was not well supported by the haplotype network profile in network. This study provided insight into the genetic basis of Nile tilapia in combining their germplasm in future