Balitoridae, a family within the Cypriniformes, inhabit torrential mountain streams in Asia. Although they have long fascinated ichthyologists for their numerous adaptations to this tumultuous environment, the evolutionary history of this group remains poorly understood. In this study, we investigate the evolutionary relationships of the balitorids with particular attention to the phylogenetic placement of two balitorid species, Yaoshania pachychulis and Erromyzon kalotaenia. Both species have extremely limited distributions, they are limited to Mt. Dayaoshan of the Pearl River in China and require dedicated conservation plans. However, little is known about their evolutionary relationships to other balitorids. Here, we examined the evolutionary relationships of Y.pachychulis and E.kalotaenia to each other and other balitorids through sequencing the complete mitochondrial genomes of nine balitorid individuals. For the newly sequenced balitorids, the length of the whole mitogenome, gene arrangement and their base composition are similar to those of other bony fishes. Analyses based on these newly sequenced mitogenomes and an additional 50 previously published mitogenomes show that Y.pachychulis and E.kalotaenia cluster as different clade within the subfamily Gastromyzontinae. The genetic distance between these two species ranges from 0.127 +/- 0.003 to 0.132 +/- 0.004 which is slightly higher than that between some genera (e.g. the distance between Vanmanenia and Metahomaloptera is 0.127 +/- 0.004). Therefore, it is reasonable to assign Y.pachychulis and E.kalotaenia to different genera. Phylogenetic signal assessment suggested that ND1, ND4 and ND5 genes as well as their concatenated subsets perform relatively well in reconstructing the Cobitoidea phylogeny. The divergence time estimation indicated that the balitorids distributed in Mt. Dayaoshan might have originated and evolved following the flattening and uplifting of the Yunnan-Guizhou Plateau during the late Miocene to late Pliocene.