The complete mitochondrial genome was sequenced from the freshwater cyprinid fish, Microphysogobio koreensis. The genome sequence was 16,606 bp in size, and the gene order and contents were identical with other cyprinid species. Of 13 protein-coding genes (PGCs), three genes (CO2, CO3, Cytb) had an incomplete stop codon as shown in other cyprinid fishes. The base composition of M. koreensis showed anti-G bias (13.79% and 10.16%) on the second and third positions of PCGs.