Pterocryptis anomala (Siluridae) is an endemic fish species that is distributed in the drainage basins of Southern China. In this study, we reported the complete mitochondrial genomes (mitogenomes) of two P. anomala specimens from different rivers using next-generation sequencing. The gene composition and the structural arrangement of the mitogenomes were similar to those of most other teleosts, although we examined a longer length of control region in these mitogenomes than that in most of published Siluridae mitogenomes. Phylogenetic analyses combining our novel sequences with published mitogenomes and mitochondrial cytochrome c oxidase I (COI) sequences indicated the monophyly of Pterocryptis and a sister relationship between species P. anomala and P. cochinchinensis. However, the monophyly of Pterocryptis was not very robust as a limited number of species were included in our analyses. Additionally, we uncovered that a hidden diversity might occur in P. anomala populations. The likely causes for this cryptic diversity might be the geologic movements of intense uplift of the Qinghai–Tibetan Plateau and evolution of Asian monsoons, as well as low vagility of P. anomala. Our results yielded crucially important insights into the genetic resources, phylogeny and diversity of this endemic species.