Four Japanese oak species in the section Prinus (Quercus mongolica var. crispula, Q. serrata, Q. aliena, and Q. dentata) share nine cpDNA haplotypes. These haplotypes have been grouped into two in northeastern Japan (Haplotypes I and II) and southwestern Japan (Haplotypes III to IX) with the boundary at the center of Honshu. In order to determine the boundary on the Pacific coast, we newly sampled Q. mongolica var. crispula and Q. serrata around Hakone and in Boso Peninsula, respectively and determined the trnQ-trnS spacer sequence. We also determined the sequence for all the nine haplotypes and re-defined the haplotypes based on newly found nucleotide substitutions. Ichihara City population possessed Haplotype I and Haplotype II, whereas, Kintoki-san population possessed Haplotype II and Haplotype III. This finding shows that the boundary of the two groups on the Pacific coast could be located at Hakone, and that the boundary of the distribution of Haplotype I occurs at Ichihara City in Boso Peninsula.