The population size of the sika deer Cervus nippon on Hokkaido Island of Japan had been remarkably reduced because of heavy hunting pressure since the beginning of Meiji Period and effects of heavy snow in 1879 and 1881. After that, the number of sika deer in Hokkaido has increased gradually due to the protection by the Hokkaido government. In the present study, in order to investigate the bottleneck effects, we analyzed ancient mitochondrial DNA (mtDNA) on sika deer bones excavated from archaeological sites just before Meiji Period. On 86 of 113 bones from 13 archaeological sites of Ainu Culture Period (17–19th centuries), 602 base-pair fragments of the mtDNA control region were successfully sequenced. Consequently, we found three new haplotypes (g-, h- and i-types) which had not been identified in modern sika deer. In addition, four haplotypes (a-, b-, c- and d-types) identified from modern sika deer were also found in the archaeological deer. The new haplotypes and previously reported hapoltypes from sika deer of Hokkaido were phylogenetically much closer to each other, compared with those of modern sika deer from Honshu, Kyushu and the Chinese continent. Geographical distribution patterns of haplotypes of the ancient population were different from those of the modern population in Hokkaido. Our findings indicated that their genetic diversity was reduced through the bottleneck and that population structures of sika deer were changed widely in Hokkaido due to genetic drift.