Inter-populational heterogeneity of the Neolithic Jomon hunter-gatherers of Japan was examined via 21 non-metric dental traits. Skeletal samples from nine local sites and five regional groups of the middle to final stages of the Jomon period were analyzed, and inter-site comparisons were made among five representative sites (Ubayama, Nakazuma, Ikawazu, Yoshiko, and Tsukumo). Statistically significant differences were found in 4/21 traits in the inter-site comparisons, and in 5/21 traits in the inter-regional comparisons between the Hokkaido, Tohoku, Kanto, Tokai, and Sanyo groups. Smith’s distances suggest that the inter-regional differences within the Jomon assemblages are minor when compared with differences from the non-Jomon samples such as the Yayoi immigrants, Kofun, and modern Japanese. Furthermore, examination of the wider geographical variation of the Jomon people (eastern versus western) revealed significant differences in only 2/21 traits. Distance analysis showed that the eastern and western Jomon groups clustered together, and exhibited the greatest affinities with present-day Southeast Asians among comparable East Asian and Pacific population samples. The Jomon people can be collectively regarded as relatively homogeneous, within the broader context of East Asian and Pacific intra-population variation.