The striped field mouse (Apodemus agrarius) is one of the most common mammals in Korea, however, limited research has focused on the population structure and biogeography of this mouse throughout Korea. In addition, the taxonomic status of the species remains unresolved. The objectives of our study were to address the inadequacies in understanding the population structure, biogeography, and taxonomic status of A. agrarius. We collected 160 samples from 13 localities throughout the South Korean Peninsula, two nearby islands and two remote islands. We used five microsatellite loci and estimated genetic diversity measures and populations divergence estimates (i.e. F-ST and R-ST) to address the objectives. Except for populations on the two remote islands, Jeju and Heuksan, the populations on the peninsula and nearby islands indicated low F-ST and R-ST values. The population structure based on microsatellite loci supported only one subspecies opposing three subspecies reported previously on the Korean Peninsula and nearby islands. However, populations on Jeju Island and Heuksan Island showed subspecific differences from each other and the populations on the Korean Peninsula and nearby islands. The information reported on the population genetics of the striped field mouse in Korea will allow resolving the taxonomy and biogeography of this species.