The Rhynchocypris oxycephalus (Cypriniformes: Cyprinidae) is an ecological important fish in East Asia. In this study, we firstly sequenced the complete mitochondrial genome of R. oxycephalus. The mitogenome is 16,606 bp in length, including 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and two non-coding regions (origin of light-strand replication and control region). The gene content and order is in accord with the common vertebrate form. The nucleotide base composition of H-strand is 28.4% A, 27.2% T, 26.4% C and 18.0% G. The complete mitochondrial genome data would be useful for further studies of genetics, conservation biology and adaptive evolution of R. oxycephalus.