Abstract: The Onychostoma belongs to cyprinid group and contains 19 species from essentially morphological classification. However, the molecular phylogenetic relationship of Onychostoma, was not very clear. Here, we presented molecular phylogenetic analysis of 8 species in Onychostoma based on the whole mitochondrial genome sequence with Danio rerio and Spinibarbus denticulatus as outgroups. The results indicated that Onychostoma did not appear monophyletic which included 3 groups: Onychostoma macrolepis, Onychostoma lini andOnychostoma barbatum. O. barbatulum in clade 1, Onychostoma gerlachi and Onychostoma simum in clade 2, Onychostoma rara and Onychostoma alticorpus in clade 3. The result was roughly the same as the traditional morphological classification, which divides Onychostoma into three branches. The mitochondrial whole genome was firstly used in Phylogenetic research of Onychostoma and filled the shortage of Phylogenetic studies of this genus.