To investigate the genetic variation of Jomon dogs (Canis familiaris) in Japan, partial sequences of the mitochondrial DNA (mtDNA) control region were determined from dog bone remains, which were excavated from two Jomon-period archaeological sites, the Kamikuroiwa Rock Shelter site in Ehime Prefecture (Shikoku Island) and the Higashimyo site in Saga Prefecture (Kyushu Island), Japan. Of seven individuals from the Kamikuroiwa Rock Shelter site, the mtDNA sequences from two individuals were successfully determined. Comparison of the resultant 215 base pair sequences with previously reported sequences showed that one of these two individuals had a new haplotype, named KRA1, and that the other had the previously reported M1 haplotype. For the Higashimyo site, three of11 individuals yielded successful sequences. Two of these three individuals shared M1 and the other one had M20, both of which are haplotypes previously reported in modern Japanese dogs, but had not been found in any Jomon dogs. The success rate in the present study was 27.8% (5/18 samples). It is noticed that the three mtDNA haplotypes (M1, M20 and KRA1) were found in Jomon dogs for the first time. In addition, sequence data were obtained from Jomon dogs in Shikoku for the first time. The results suggest that the genetic lineages in the Jomon dog populations were more polymorphic than previously reported, and that at least some maternal lineages shared in the Jomon period descended to modern dogs on the Japanese islands.