We have characterized the complete mitochondrial genome of a Korean ikonnikov's bat species, Myotis ikonnikovi. Total length of the mitogenome is 16,585 bp with a total base composition of 34.0% A, 30.4% T, 22.8% C and 12.8% G. The mitogenome consists of 13 protein-coding genes, 2 rRNA (12S and 16S RNA) genes, 22 tRNA genes and 1 control region. The mitogenome of M. ikonnikovi exhibited similar features compared with the previously determined mitogenome of a Myotis species, M. formosus. The results will contribute to our understanding of the mechanisms underlying mitogenome evolution in the genus Myotis bats.