Ancient mitochondrial DNA (mtDNA) mainly from Jomon Period Sus scrofa bone specimens (6,100–1,700 years old) was examined to clarify the genetic relationships between prehistoric and contemporary S. scrofa on Hokkaido, Honshu, Sado, and Izu islands of the Japanese Archipelago. Phylogenetic analysis of the mtDNA control region (574 bp) and analysis of pairwise nucleotide differences between prehistoric and contemporary S. scrofa sequences showed the following relationships between these groups: (1) a group genetically similar to contemporary Japanese wild boars was found mainly on Honshu Island, Hokkaido Island, and the Izu Islands, and (2) a monophyletic group distinct from contemporary Japanese wild boars was found on Sado Island. These results suggest that prehistoric people introduced S. scrofa from Honshu Island to Hokkaido Island and the Izu Islands. The estimated divergence times between the prehistoric Sado group and the other prehistoric S. scrofa is approximately congruent with the geological isolation of Sado Island from Honshu Island. Our results suggest that this extinct S. scrofa population was present on Sado Island as recently as around 2,000 years ago.