Abstract: Channa gachus is a tropical and subtropical species of freshwater carnivorous fish, and they have highly ornamental and economic values in original origins. C. gachus usually live in slow-flow rivers, ditches and ponds. As for in China, they mainly inhabit in the Irrawaddy River, the Nujiang River and the Lancang River in Yunnan Province, as well as in some rivers in Hainan Province. Due to the extensive hydraulic construction, river pollution and overfishing, the number of the fish has sharply decreased. To develop effective strategies of protecting its germplasm, it is important to investigate the genetic variance and the structure of the population of this species. Previous studies have focused on the chromosome and the isoenzyme of C. gachus, as well as the phylogenetic relationship between C. gachus and other species in the same genus. However, the genetic backgound of this fish remains obsecure. In the present study, we sequenced 411 bp segments of mitochondrial DNA control regions of 74 C. gachus indi-viduals collected from 9 populations in the Lancang River in Yunnan Province, and the Nandu River, the Wanquan River and the Changhua River in Hainan Province of China. We observed 52 mutations of nucleotide acids and 20 haplotypes. There were 3 haplotypes shared by 5 populations in Hainan Province, whereas all other haplotypes were unique in each population. We observed 3 distinct lineages in the Kimura2-parameter-based Neighbour-Joining tree. One of them was from Yunnan, and the other 2 were from Hainan-one was the Maoyang population from the Changhua River, another was from the Nandu River and the Wanquan River, and the rest two populations were from the Changhua River. The pairwise fixation index Fst was 0.786-0.672, the gene flow was 0.153-0.244, and the inter-clade variation accounted for 74.352% of the total variation. These data indicated a significant genetic differentiation between the 3 clades. The differentiation time of the 3 clades was 2.070-0.350 Ma. The differentiation of the Hainan and Yunnan groups might have been affected by the uplift of Yunnan-Guizhou Plateau and the separation of Hainan Island from Mainland China. Following the isolation from the Maoyang population, the 2 distinct lineages in Hainan Island might be formed under the impact of the uplift of Wuzhi Mountains. Parameters such as the Fst (0.765, P0.01), the gene flow(0.149) and the genetic variation(70.360%) between the Yunnan and Hainan groups indicated a high degree of differentiation. In contrast to the high overall genetic diversity(Hd=0.9030.016, =0.0360.003), the nucleotide diversity within individual populations was much lower. The nucleotide diversity of the Qiongzhong and Shibi populations was the highest(0.008), and the Mengla population had the lowest diversity(0.000). The high overall genetic diversity might result from a mixture of multiple lineages. In the parsimony network of C. gachus, the haplotypes from Yunnan Province were on one side, and the haplotypes from the Maoyan population were in the middle, and the remaining from Hainan Island were on the other side. The distribution of the haplotypes showed an atypical star-shape in the parsimony network diagram. The neutrality tests gave a non-significant negative value. Moreover, the mismatch distribution analysis displayed a multimodal distribution. These results suggested that there was no significant expansion in the population in recent history. Because there are 3 lineages of Chinese C. gachus, we recommended that they should be treated as 3 separate protected units.