Abstract: The Chinese longsnout catfish is a semi-migratory fish which is commercially valuable in China. Due to overfishing, environmental pollution, and other human disturbances, the populations of this species have declined rapidly and disappeared in many river systems in the past decades. Currently, the Chinese longsnout catfish mainly inhabits the main streams of the Yangtze River and rarely found in lakes. At present, the Chinese longsnout catfish achieved appropriate scale farming in Sichuan, Guangdong and other places. However, seldom study was reported about analysis of population genetic structure using molecular markers. To protect and exploit this rare species effectively, investigations on population structures, resources and artificial reproduction have been conducted. In this study, the mitochondrial DNA control region were used to analyze genetic diversity and structure of 7 cultivated and natural populations of Chinese longsnout catfish collected from Meishan, Shishou, Huainan, Chongqing, Wuhan, Anqing and Nanjing named Meishan population, Shishou population, Huainan population, Chongqing population, Wuhan population, Anqing population and Nanjing population separately. The results showed the length of this region (D-loop) contained 790 bp nucleotides and the T, C, A and G contents were 31.5%, 25.3%, 29.1% and 14.1% respectively. Twenty-seven nucleotide sites and 18 haplotypes were found in 3 cultivated populations of Chinese longsnout catfish. Thirty-five nucleotide sites and 36 haplotypes were found in 4 natural populations of Chinese longsnout catfish. The average haplotype diversity and nucleotide diversity of cultivated populations of Chinese longsnout catfish were relatively low (Hd=0.8867±0.0013, Pi=0.0056±0.0013). The level of genetic differentiation was relatively low (0.0014—0.1125). Molecular phylogenetic tree and statistical parsimony network constructed by NJ method and statistical parsimony principles showed individuals from the same stock did not cluster together, and individuals from three different stocks nested with each other. These results suggested gene flow was sufficient between breeding populations and wild populations. They had no obviously genetic differentiation between breeding populations and wild populations. The genetic diversity of the cultivated populations of Chinese longsnout catfish was low.