Population affinities and biological variation in human skeletal series associated with the Okhotsk culture from Hokkaido and Sakhalin Islands from the 5th to 12th centuries AD are investigated using 19 nonmetric cranial traits. The Okhotsk crania have a higher frequency of the supraorbital foramen than the Hokkaido Ainu and Jomon, while the frequency of the transverse zygomatic suture vestige in the Okhotsk is as high as in the Jomon. The mean measure of divergence between the northern and eastern Okhotsk cranial assemblages is small and insignificant. The method of Relethford and Blangero [Relethford J.H. and Blangero J. (1990) Human Biology, 62: 5–25] suggests that the eastern Okhotsk had a larger Rii value (distance from the centroid) and a lower observed variation than the northern Okhotsk, indicating that the eastern Okhotsk lost phenotypic variability. These results further reaffirm the affinity between the Okhotsk skeletal series and Northeast Asian series such as the Neolithic Baikalian and Amur. Finally, the results of analyses of nonmetric cranial variation demonstrate a close relationship between the Okhotsk, Ainu, and Jomon series that suggests that the Jomon and Ainu were closer to the Okhotsk than to other Northeast Asian series prior to any admixture.