Abstract: We amplified the mtDNA D-loop sequence in two stocks of Leuciscus waleckii Dybowski in Dali Lake and Ganggeng Lake in Inner Mongolia, having obtained 896 bp gene sequences; the average contents of T, C, A and G of homological fragments were 32.0%, 32.2%, 21.3%, 14.5% and 32.0%, 32.2%, 21.4%, 14.5% in Dali Lake stock and Ganggeng Lake stock, respectively, with no significant difference. The inter- and intra-population of the two stocks had high degree of sequence polymorphism. There were 33 variable sites in 896 D-loop gene loci in the two stocks, and the rest sites were more conservative. The D-loop genes of 30 fish in Dali Lake contained 21 polymorphisms/mutations and 11 haplotypes; while those in Ganggeng Lake contained 31 polymorphisms /mutations and 17 haplotypes. The diversity of D-loop gene in Ganggeng Lake stock was higher than that in Dali Lake stock. Genetic distance calculation shows that the average genetic distance between Ganggeng Lake and Dali Lake stocks was 0.007 0 (Dali Lake: 0.003 6, Ganggeng Lake: 0.007 4). The genetic distance of the D-loop gene in Ganggeng Lake stock was greater than that in Dali Lake stock, and the evolution speed of the former was faster than that of the latter.