The genetic structures of four Siberian Dace (Leuciscus leuciscus baicalensis) populations (Qinghe QH, Haba River HBH, 185 Regiment 185T and Ulungur Lake WLG, Fig. 1) from Irtysh River were analyzed by mtDNA Cyt b gene marker. A total of 1 109 bp sequences were obtained and 54 haplotypes were found among 77 individuals including 7 shared haplotypes. Total haplotype diversity (Hd), total nucleotide diversity (π) and average nucleotide difference (K) were 0.981 9, 0.008 21 and 9.091 (Table 1), respectively. The haplotype and nucleotide diversity of 185T were the highest, whereas those of QH were the lowest. The genetic distance among four populations ranged from 0.006 to 0.011. Neighborhood-joining (NJ) phylogenetic tree of all haplotypes based on Kimura 2- parameter method was divided to three branches (Fig. 2). There was no significant correlation between genetic relationship and geographical distance. AMOVA analysis showed differences among Siberian Dace populations were extremely significant (P < 0.01, Table 3). The gene flow (Nm) between QH and WLG was much higher than other populations, indicating Ulungur River was the genetic communication channel between them (Table 2). Although nucleotide mismatch distribution was bimodal, both sum of squared deviation (Q) and raggedness index (r) were not significant (P > 0.05, Fig. 3). Meanwhile, Tajima′s D and Fu′s Fs neutral test gave positive values, in combination with high haplotype diversity and low nucleotide diversity, authors still considered Siberian Dace experienced population expansion. Applying 0.76% divergence rate of Cyt b gene sequence in Cyprinid fish, the divergence of Siberian Dace occurred about 1.97 Ma years ago during the middle-late Pleistocene. It was supposed that geographical isolation and fusion caused by glaciation and frequent paleo-earthquake in Altai region were the important reasons for population expansion.