It is now generally held that the Neolithic Jomon people with generalized craniofacial features occupied the entire Japanese archipelago. Around 2300-1300 years BP, migrants from somewhere in eastern Asia to the southwestern part of Japan admixed with the indigenous Jomon descendants. Based on this population history, it is expected to find clinal variation of genetic as well as phenotypic traits over space and time, as well as population groups related to the previous inhabitants over which the present one has been superimposed at the periphery of the expansion of migrant lineages, the Tohoku region. Taking these hypotheses into account, the present study focuses on the pattern of spatial and temporal craniometric variation to address the process of population growth, expansion, and microevolution during the last 2000 years, with special reference to the population history of the Tohoku region. The results obtained support the 'dual structure model' for the origin and affinities of modern Japanese. Turning to the situation of the Tohoku region, one may conclude that the relatively close morphological affinity of Tohoku Kofun and, to a lesser extent, Tohoku Edo with the recent Ainu should not be regarded as an evidence of the close population relationships (ancestraldescendant relationships) but a possible differential retention of common ancestral characteristics.