We analyzed mitochondrial DNA (mtDNA) restriction fragment length polymorphisms of medaka (Oryzias latipes) from 15 localities in South Korea and three localities in China. The analysis revealed nine mtDNA haplotypes of two distinct clusters; cluster A and B. Cluster A and B consisted of six and three haplotypes, respectively. Furthermore, we analyzed other specimens from 45 localities in South Korea, using two restriction enzymes, to investigate the detailed geographic distribution of these mtDNA haplotypes. The findings revealed a strong geographical association in mtDNA types. The geographic distributions in mtDNA types of cluster A and B closely agreed with the previously described ranges of the East Korean Population and the China-West Korean Population defined by allozymes. Such agreement between independent elements of the genome may be expected if the two populations had evolved in complete isolation at some time in the past.