Recent overpopulation of the sika deer (Cervus nippon) in Hokkaido has resulted in expansion of their distribution from eastern to western parts of this island. To assess changes of genetic population structures of the Hokkaido sika deer, mitochondrial DNA control sequences (602 base-pairs) from 283 animals collected from central and western Hokkaido were analyzed. Based on transitional substitutions (A < – > G) at four nucleotide sites, five haplotypes were identified. One haplotype was newly found in the present study, and the other four haplotypes referred to those reported previously. The distribution patterns of haplotypes showed characteristic changes of genetic population structures, compared with the past distribution of haplotypes. In northern Hokkaido, for instance, the population around the Okhotsk Sea-coastal region has clearly expanded to the Japan Seacoastal region. The population around the Ishikari-lowlands and the Hidaka mountains has increased within these areas, and it is not likely that the increase is directly caused by the immigration from eastern Hokkaido.