This study reevaluates the relationship between the prehistoric Jomon and modern Ainu based on 18 nonmetric cranial traits. Although the two Ainu series from the northeast coast and central/southern regions of Hokkaido Island are always associated with Jomon, significant differences between the Ainu and Jomon were detected in the frequencies of seven traits: metopism, supraorbital foramen, ovale–spinosum confluence, hypoglossal canal bridging, jugular foramen bridging, biasterionic suture vestige, and occipitomastoid bone. Regarding these traits, the Ainu series are more similar to the Okhotsk than to the Jomon series. A broad comparison among pan-Pacific populations confirms the maintenance of distinctive morphologies in the remote regions of group ranges, as represented by the Jomon and to a lesser extent the recent Hokkaido Ainu. The Ainu occupies an intermediate position between Jomon and Northeast Asians on the one hand, and between Jomon and the Native Americans on the other. The pattern of temporal change between Jomon and Ainu, together with clinal variation among the three Ainu series from Sakhalin Island, the northeast Hokkaido coast, and central/south Hokkaido shown in the present study, indicate possible admixture between the ancestors of recent Ainu and northern groups such as the Okhotsk people in the post-Jomon periods.