Abstract: Leptobotia microphthalma is a small freshwater fish, endemic to the Upper Yangtze River, and its distribution is limited. In this study, mitochondrial DNA cytochrome b (cyt-b) and control region sequences were used to investigate the genetic diversity and structure of L. microphthalma populations. A total of 108 fishes were collected from Yibin and Jiangjin stations in the upper Yangtze River. In spite of limited distribution, the population exhibited a high level of genetic diversity; the average haplotype diversity (H_d) and average nucleotide diversity (P_i) were 0.889 and 0.00382 in cyt b and 0.958 and 0.00420 in control region, respectively. Hierarchical analysis of molecular variance (AMOVA) showed no significant genetic differentiation among sampled populations (F_ST<0.05). The high average gene flow (N_m) value revealed frequent genetic exchange between populations. Three haplotype groups with distinguishing mutant steps were identified from network diagram, and great genetic differentiation (F_ST>0.25) existed among them, suggesting genetic divergence within population. Nucleotide mismatch distribution and the neutral test (Tajima’s D) result showed that there probably existed no population expansion of L. microphthalma in history.

Key words: lake ecosystem, modern surface sediment, diatom functional group, evolutionary history., spatial distribution