Micropercops swinhonis is a freshwater sleeper widely distributed in the Yangtze River drainage and other main drainages in northern China. We collected individuals from Songhua Jiang, Liao He, Hai He, the lower drainage of Yellow River (Puyang), Gaoyou Hu and the Yangtze River drainage (Shaoyang Zishui, Honghu, Jingzhou, Jiangjiang, Chaohu, Taihu, Langxi and Dongting Hu). Population genetic structure and divergence of M. swinhonis among different areas were investigated by analysing the sequences of mitochondrion cytochrome b (cyt b) and control region (D-loop). Concatenating sequences of cyt b and D-loop of 88 individuals resulted in 63 haplotypes and 133 variable sites. AMOVA, SAMOVA, analysis of haplotype network and phylogenetic reconstruction all supported splitting M. swinhonis into three groups:Shaoyang (Zishui; clade A), Taihu (clade B) and the population of other areas (clade C), which could be further divided into three subclades. Mismatch distribution revealed that populations from Jingjiang (Fu's FS:-4.119, P=0.009) and Honghu (Fu's FS:-2.814, P=0.016) probably experienced a recent expansion.