We have sequenced the complete mitochondrial genome of the Kikuchi's minnow, Aphyocypris kikuchii (Oshima 1919), which is an endemic species to Taiwan. The complete mitochondrial genome is 16,601 bp in size, containing 37 genes coding for 13 proteins, 2 rRNAs, 22 tRNAs, and 1 control region. It has the typical vertebrate mitochondrial gene arrangement. The sequence information could play an important role in resolving the conflict on its current taxonomic position and preservation of genetic resources for helping conservation of the endangered species.