The complete mitochondrial genome of the stone loach Triplophysa stoliczkae is 16,571 bp in size, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a noncoding control region. As in other vertebrates, most mitochondrial genes are encoded on the heavy strand, except for nd6 and eight tRNA genes which are encoded on the light strand. The overall base composition of the heavy strand of the T. stoliczkae mitochondrial genome is A: 28.1%, T: 29.0%, C: 25.0%, and G: 17.9%. The alignment of the Triplophysa species control regions exhibited high genetic variability and rich A+T content.

The complete mitochondrial DNA genome of Ptychobarbus kaznakovi was sequenced and characterized. The genome is 16,842 bp in length. Similar with most teleosts, it has two ribosomal RNA (rRNA) genes, 13 protein-coding genes, 22 transfer RNA (tRNA) genes, and one displacement loop (D-loop) region. Conserved sequence blocks, including ETAS, CSB-B, D, E, F, and CSB1-3, were identified in the D-loop, which is similar to other species in Cypriniformes. Nevertheless, a 55 bp tandem repeat array was also identified at 3′ end of the D-loop, which is the first finding in Schizothoracinae. Phylogenetic analysis showed that the species of Ptychobarbus (P. dipogon and P. kaznakovi) formed a monophyletic group and represented close relationship to the species without scales in Schizothoracinae.