In this study, nine nonmetric cranial traits were recorded for ancient human remains excavated at early prehistoric (the late Pleistocene, early Holocene, and Pre-Pottery Neolithic) and late prehistoric (the Neolithic and early Iron age) archeological sites in northern Vietnam. The comparative samples consist of prehistoric and early historic crania from the lower Yangtze River basin, together with recent cranial series from Vietnam, Thailand, South China, and Australia. The results, based mainly on the measure of divergence, are as follows: (1) the early prehistoric northern Vietnam group is distinct from the subsequent inhabitants of northern Vietnam and neighboring populations; (2) the cranial series of northern Vietnam and the surrounding region from the late prehistoric to recent times through early historic period exhibit relative homogeneity, suggesting population continuity; (3) the recent Han Chinese from southern China, one of the possible representatives of East Asians, are relatively distant from all groups from the prehistoric age onwards; and (4) a clear separation of Aboriginal Australians from all the comparative samples, including the early prehistoric northern Vietnamese, is evident. These findings suggest partial support for the two opposing hypotheses, i.e. the two-layer model and the regional-continuity model, for the population history of Southeast Asians, at least, in the northern Vietnamese region. This may be further compatible with the recent hypothesis for modern human dispersals: an earlier out-of-Africa expansion of Australians than other contemporary Eurasians including Southeast Asians.