The germplasm and genetic diversity of three species introduced in the Sayram Lake of the Xinjiang Province, Baikal omul () and broad whitefish (), were characterized using DNA barcoding of the CO I gene. A total of 15 haplotypes were found in the three species of interest, of which five haplotypes were identified for the Baikal omul, seven for broad whitefish, and five for peled; the latter two shared two common haplotypes, indicative of gene introgression from , based on the haplotype analysis. Construction of a phylogenetic tree using the neighbor-joining method showed that 15 haplotypes were divided into three different branches, and each branch was respectively clustered with the published sequences, which indicated that the species introduced to the Sayram Lake had still been maintaining good provenance characteristics; , which had the largest genetic distance (0.027) to its close species , had clustered independently. Genetic diversity of the three species is moderate, and C. peled because of the possibility of hybridization between . We recommend that the fishery production department in the Sayram Lake continue planning the breeding, fishing, and other production activities scientifically, and importing advanced germplasm identification technology to avoid germplasm contamination caused by artificial hybridization. Meanwhile, it is necessary to improve and maintain the genetic diversity of the species, thus, ensuring the sustainable development of fishery in the lake.