We obtained 282 base pairs of sequence for the mitochondrial control region of 70 individuals of Korean striped field mice Apodemus agrarius coreae and Apodemus agrarius chejuensis to determine the levels of genetic divergence between these morphologically distinct taxa. The DNA sequences showed more genetic diversity (pi) in A. agrarius coreae (2.98%) than in A. agrarius chejuensis (1.86%). Our data do not support the current concept that the two morphotypes are different species, but phylogenetic analysis indicates that animals of A. agrarius coreae with large body size from Wan Island cluster with the large-bodied A. agrarius chejuensis, and should be included in that taxon. As currently accepted A. agrarius coreae is not strictly monophyletic, because the large-bodied samples cluster within the range of mitochondrial variation of A. agrarius chejuensis. The fact that the two morphotypes do not share mitochondrial haplotypes (chi2=66, P < 0.001) suggests that there is little gene flow between them. A molecular clock estimate suggests that the two subspecies might have been isolated at the time of separation of the islands from the mainland.