This study examined the craniometric traits of the Edo-period (AD1603–1867) human skeletons from the Hitotsubashi site in Tokyo, compared them with temporally and socially various populations, and attempted to detect the morphological differentiation patterns that the Edo-period Japanese exhibited over time and under those social/environmental conditions. The materials measured here were the townsmen's crania from the Hitotsubashi site, which were dated back to the early half of the Edo period. The observations revealed that the Hitotsubashi samples were more dolichocephalic than any other Edo series and were different from subsequent Edo series in terms of larger maximum cranial length and smaller maximum cranial breadth. The Hitotsubashi samples were definitely in contrast with those of Tentokuji and Shirogane, both of which included a samurai (warrior) class of the late to final Edo period and exhibited the most brachycephalic crania. It is reasonable to assume that the temporal and social situations were possibly related to the observed cranial variation and that the temporal changes in cranial dimensions in pre-modern Japan might have reflected the nutritional and environmental conditions. Copyright © 2010 John Wiley & Sons, Ltd.