Previous phylogenetic analyses of the Chinese sisorid catfishes have either been poorlyresolved or have not included all the 12 sisorid genera. Here, we successfully assembled the firstcomplete mitochondrial genome of the sisorid fish Glyptothorax macromaculatus. Based on thisnovel mitochondrial genome and previously published mitochondrial genomes in the Sisoridae,we generated maximum likelihood and Bayesian phylogenies. We dated our preferred topologyusing fossil calibration points. We also tested the protein-coding genes in the mitochondrialgenomes of the glyptosternoid fishes for signals of natural selection by comparing the nucleotidesubstitution rate along the branch ancestral to the glyptosternoid fishes to other branches in ourtopology. The mitochondrial sequence structure of G. macromaculatus was similar to those knownfrom other vertebrates, with some slight differences. Our sisorid phylogenies were well-resolvedand well-supported, with exact congruence between the different phylogenetic methods. This robustphylogeny clarified the relationships among the Chinese sisorid genera and strongly supportedthe division of the family into three main clades. Interestingly, the glyptosternoid divergencetime predicted by our molecular dating analysis coincided with the uplift of the Tibetan Plateau,suggesting that geology may have influenced speciation in the Sisoridae. Among the mitochondrialprotein-coding genes, atp8 may have most rapidly evolved, and atp6 may have been subjected topositive selection pressure to adapt to high elevations. In summary, this study provided novel insightsinto the phylogeny, evolution and high-altitude adaptions of the Chinese sisorid fishes.