The Yangtze River is the longest river in Asia and the third-longest in the world with more than 400 fish species existed. Chishui River is a major tributary of the upper Yangtze River and plays a vital role in the fish resources protection of the Yangtze River. Currently, evolutionary process of Longnose Gudgeon (Saurogobio dabryi), a fish species widely distributed in Asia, is not known. In this paper, 76 Longnose Gudgeon individuals collected from the upper Yangtze River (marked as Yibin population and Hejiang population respectively) and its tributary Chishui River (marked as Chishui population) were studied by using mitochondrial DNA cytochrome b gene sequences to analyze its genetic diversity and population history. The main results are: 1) The analyzed cytochrome b gene sequences were 1 097 base pairs in length, with 28 variable sites containing 18 parsimony informative sites. Besides, 26 haplotypes were identified from 76 individuals (Table 1), which showed relatively high haplotype diversity (Hd = 0.872) and low nucleotide diversity (Pi = 0.004 0) respectively (Table 2); 2) Three populations shared several common haplotypes. Phylogenetic trees based on haplotype dataset by using NJ, ML and BI methods showed that all haplotypes from the upper Yangtze River and Chishui River were not clustered separately according to the geographical distribution. Instead, they mixed with each other (Fig. 2). Network diagram was also constructed, indicating that all haplotypes had a star-shaped distribution, and original haplotype and evolutionary center could not be detected (Fig. 3). 3) based on obtained haplotype frequencies, genetic differentiation index (FST) values among three populations maintained at low levels (﹣0.029 3, 0.028 0 and 0.025 8, respectively) and analysis of molecular variance (AMOVA) showed that overall population divergent variation of Longnose Gudgeon in the upper Yangtze River was mainly from within populations (80.00%) (Table 3), indicating that Yibin population, Hejiang population, and Chishui River population belong to the same population with frequent gene flow; 4) Neutral test, mismatch analysis (Fig. 4) and BSP (Bayesian skyline plot) analysis (Fig. 5) showed that overall S. dabryi population from the upper Yangtze River and Chishui River experienced expansion during 0 to 0.025 Ma BP (before present).