A close resemblance between the prehistoric Jomon and modern Ainu in skeletal morphology is now widely accepted. To confirm that the Ainu are actually descended from the Jomon, all available skulls of the Epi-Jomon period in Hokkaido, roughly contemporaneous with the Yayoi and Kofun periods in mainland Japan (ca. 300 BC-700 AD), were intensively investigated in terms of metric and nonmetic variations. Craniometric analyses based on Mahalanobis' D2 distance and canonical discriminant analysis as well as cranial nonmetric analyses based on Smith's Mean Measure of Divergence and likelihood ratio analysis yielded the results that the Jomon, Epi-Jomon and Ainu are closely related with each other and distant from the mainland Japanese including the northern Kyushu Yayoi of continental lineage. From these results, we concluded that the genetic influence of Yayoi immigrants on the Epi-Jomon appears to have been very limited, if any, and the Epi-Jomon inhabitants in Hokkaido were transitional in microevolutionary change from the Jomon in eastern Japan to the Hokkaido Ainu.