Rhynchocypris oxycephalus (Sauvage and Dabry de Thiersant, 1874) distributed in East Asia is small cold-water fish. We completed whole mitochondrial genome of R. oxycephalus caught in Korea. Its length is 16,583 bp, which is shorter than those of three mitochondrial genomes from China and Japan. Three hundred ninety seven of 1,278 SNPs and 27 of 44 INDELs are Korean R. oxycephalus specific. It contains 13 protein-coding genes, 2 rRNAs and 22 tRNAs and its GC ratio is 44.5\%. Phylogenetic analysis presents genetic diversity of R. oxycephalus originated from Korea, Japan, and China.