There has been much debate on the taxonomy of Schizothoracids. Phylogenetic study provides an effective way to solve taxonomic problems. In this study, mitochondrial genome data from GenBank were analyzed using the maximum likelihood and Bayesian methods to investigate the phylogeny of Schizothoracids. Two data sets were applied: one was composed of 13 protein coding genes (PCGs) and the other of 13 protein coding genes plus two rRNA genes (13 PCGs & 2 rDNAs). Phylogenetic relationships were reconstructed using the multipartition and single-partition strategies, respectively, in adopting nucleotide substitution models to the data sets. The results showed a clear clustering within each of the three grades of Schizothoracids. The “primitive” Schizothoracids and the genus Percocypris of barbine fishes form a monophyletic group, while the “specialized” and “highly-specialized” Schizothoracids form the other evolutionary branch, being paraphyletic to the former. The “highly-specialized” Schizothoracids shared a most recent common ancestor with some “specialized” Schizothoracids. Our results do not support Schizothoracids as a subfamily, but support the combination of “specialized” and “highly-specialized” Schizothoracids into the Schizopygopsini tribe, while “primitive” Schizothoracids and the genus Percocypris are grouped as the Schizothoracini tribe. There was no significant improvement in solving the phylogenetic relationships of Schizothoracids when analyzing with different data sets and different data partition strategies. Time to most recent common ancestor (tMRCA) for main Schizothoracids groups was then estimated using 13 PCGs with a single-partition strategy in adopting nucleotide substitution models to data and the Bayesian method, with the geological evidence and mitochondrial DNA substitution rate as priors. The results showed that the tMRCA of Schizothoracids and Percocypris was about 13.16 Ma, suggesting that these fishes diverged at some point after the middle Miocene. The tMRCA of “primitive” Schizothoracids was about 4.94 Ma, indicating that they originated during the Pliocene. While the tMRCAs of “specialized” and “highly-specialized” groups imply that they began to differentiate from their common ancestor around 9.64 Ma ago, the tMRCA of the “highly-specialized” group suggests it originated approximately 5.40 Ma ago. Considering the geographical history of the distribution range, Schizothoracids may have originated late in the post-collisional period of the Indian and Eurasian plates, and the differentiation of main groups and speciation events in Schizothoracids could closely be related to the stage type evolution and climate fluctuation of the Qinghai-Tibet Plateau.