Abstract: Genetic diversity and population demography of Coreius guichenoti from the middle and lower reaches of the Jinsha River were investigated using mitochondrial DNA Cyt b gene and CO I gene sequences. The results showed that 91 haplotypes were identified from 393 individuals based on concatenated sequences, with relatively high haplotype diversity of (0.936±0.006) and low nucleotide diversity of (0.00489±0.00009). Phylogenetic trees and median-joining Network based on haplotypes indicate that all haplotypes from the middle and lower reaches of the Jinsha River were mixed with each other according to their geographical distribution, but exhibited three distinct haplotype lineages (Clade 1, Clade 2 and Clade 3). Clade 1 diverged at about 3.66 Ma, while Clade 2 and Clade 3 diverged at about 2.93 Ma. Analysis of molecular variance (AMOVA) showed that the larger genetic variances were within different geographical locations (96.62%) and between different haplotype lineages (81.29%), while the lesser genetic variance were between different geographical locations (3.38%) and within different haplotype lineages (18.71%). Pairwise comparisons of genetic differentiation index (F_st) among different populations ranged from –0.008 to 0.045. Except for the insignificant F_st value between PS and other locations, significant but low F_st were investigated between other two locations (F_st<0.05, P<0.05). In contrary, significant maximum genetic differentiation level was revealed between three haplotype lineages (F_st>0.25, P<0.001). Neutrality test, mismatch distribution and Bayesian Skyline Plot (BSP) all revealed that wild populations of C. guichenoti from the middle and lower reaches of the Jinsha River may have experienced the population expansion event. It may happen at 0.0007—0.0004 Ma during the Holocene small glaciers period. It suggests that the uplift of Qinghai-Tibet Plateau and the evolution of glaciers during Holocene small glaciers period may play important effect on the population demography of C. guichenoti in the Jinsha River. In order to better protect the wild resources of C. guichenoti, it was suggested to pay special attention to the three haplotype lineages of C. guichenoti in the middle and lower reaches of the Jinsha River for guiding its culture production.