This study investigates geographical and temporal variation in three sets of transverse facial flatness measurements—the frontal, simotic, and zygomaxillary indices—in cranial series dating from the Jomon to modern periods of eastern Japan (Hokkaido, Tohoku and Kanto). In Hokkaido, the Ainu retains an early condition of facial features, linking them to the Jomon and Epi-Jomon groups. On the other hand, there were sudden changes from the Jomon to Kofun and from the Edo to modern periods in the Tohoku and Kanto regions. In the Jomon and Hokkaido groups, the similarities in facial morphology probably reflect a similar lifestyle and a close genetic relationship. This contrasts with the changes seen in the Tohoku and Kanto regions, which may result not only from gene flow but also from changes in the pattern of subsistence.