More than ten species of the genus Sinocyclocheilus (Cyprinidae: Barbinae) have been found to exhibit striking variation related to cave-dwelling traits. Until now, the molecular phylogeny and evolutionary history of this genus have remained unclear. To understand the molecular phylogeny and biogeographic evolution of Sinocyclocheilus, we analyzed the complete mitogenomes of 12 Sinocyclocheilus species based on Bayesian Inference (BI) and Maximum Likelihood (ML) analyses. The results of phylogenetic analyses strongly suggest that the genus Sinocyclocheilus is a monophyletic group, and S. jii is the most basal species. Molecular clock estimates showed that the diversification of this genus occurred in the late Miocene (about 6.49 Ma), which was associated with the intensive uplift of the Tibetan Plateau. Selective pressure analyses showed the dN/dS ratios of all Sinocyclocheilus species were < 1, indicating that this genus suffered strong purifying selection on its mitochondrial function, and then adapted to the contrasting environments.