DNA was extracted from human teeth samples excavated from the Nakazuma Jomon shell midden (BC 2500) which is located north of the Kanto Plain. Part of the mitochondrial control region (233 bp) was amplified by a polymerase chain reaction. Mitochondrial DNA sequences determined from 29 individuals were classified into 9 different haplotypes defined by 17 segregating sites. The most frequent haplotype was observed in 17 individuals (58.6%). Most individuals shared the same sequence, suggesting the possibility of close maternal relationships at this site. On the other hand, the sequence diversity at the Jomon site was almost the same as the mitochondrial sequence diversity observed in modern Japanese. Phylogenetic analysis indicated that the Jomon haplotypes were scattered among modern Japanese haplotypes and did not fall into specific clusters. Both the extensive sequence divergence and the results of phylogenetic analysis showed that the Jomon people at the Nakazuma site were not a genetically homogenous population. Moreover, the magnitude of the mitochondrial. diversity observed within the Nakazuma Jomon people may indicate that severe genetic bottleneck did not occur during the formation of the Jomon population.