Family of Gastromyzontidae originates from China and Southeast Asia, which is widely distributed in the southern part of the Yangtze River. In this study, we sequenced seven fish complete mitogenomes from three of all 18 genera in the Gastromyzontidae on the Illumina HiSeq platform. Lengths of seven complete mitochondrial genome sequences varied from 16,554 to 16,574 bp, with an AT bias of 53.6-54.9%. Maximum-likelihood phylogenetic tree was reconstructed using the connected protein sequences of 13 protein-coding genes of 34 species of fish. The phylogeny revealed that the genera Gastromyzon, Sewellia, and Erromyzon were monophyletic, and other genera Beaufortia, Vanmanenia, Formosania, and Pseudogastromyzon were paraphyletic or polyphyletic. Phylogeny corrected the taxonomic status of Metahomaloptera omeiensis, which should be categorized under the family of Gastromyzontidae rather than Balitoridae, denoting the significance of this study to the overall fisheries research.