The population history of Japan has been widely interpreted in terms of an original Jomon occupation from the Neolithic period followed by admixture with Yayoi immigrants associated with the spread of rice farming agriculture from western Japan. According to this perspective, the people in areas remote from the western mainland island of Honshu, Japan would be less affected by the genes of immigrants. This article uses metric and nonmetric dental data to examine the genetic influence of immigrants among the early modern Edo and modern residents in the Tohoku district of northeastern Honshu. The results of these dental-trait analyses suggest a smaller gene flow of immigrants in Tohoku people, as compared to contemporary Japanese in the central and western parts of Japan. The metric dental data imply the gene flow from the west to the north was still due mainly to the males even in recent times. The findings of some Jomon features in the late historic and modern Tohoku tooth samples support the speculation that the ancient inhabitants of this region, in the past referred to as ‘Emishi’, are people who still have preserved genetic traits of the indigenous people.