In this study, we sequenced and characterized the complete mitochondrial genome (mitogenome) ofOnychostoma ovale. The mitogenome ofO. ovalewas 16,602 bp in length with 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a control region. The nucleotide composition of theO. ovalemitogenome was 31.47% A, 24.07% T, 15.92% G, and 28.54% C, with a higher A + T content (55.54%) than G + C content (44.46%). All PCGs began with the standard ATG codon, except for the cytochrome c oxidase subunit 1 (COX1) gene and the NADH dehydrogenase 3 (ND3) gene with GTG, while six PCGs ended with incomplete termination codons (TA or T). The Ka/Ks ratios of 13 PCGs were all less than one, indicating that they were under purifying selection. All tRNA genes were folded into the typical cloverleaf secondary structures with the exception oftRNASer(AGY), whose dihydrouridine (DHU) arm was absent. The phylogenetic trees showed thatOnychostomaandAcrossocheiluswere classified into three clades. There was a mosaic relationship betweenOnychostomaandAcrossocheilus. Moreover, the phylogenetic tree analysis showed thatO. rarumwas the closest species toO. ovale. This study can provide a useful resource for further phylogeny and population genetic analyses ofOnychostomaandAcrossocheilus.