This article presents the results of an assessment of the morphological affinities of the skeletal remains from a large mortuary assemblage, dated to Iron Age, in Phum Snay, a village in Banteay Meanchey Province, northwest Cambodia. The purpose of the research is to address the origin of these pre-Angkorian people. Multivariate comparisons using cranial and dental metrics, as well as dental nonmetric traits, demonstrate that the characteristic affinities intermediate between the early Holocene Hoabinhian groups akin to Australo-Melanesians and the present-day people in the mainland Southeast Asia. This finding suggests that the ancient people of Phum Snay preserved genetic traits of early indigenous populations, whereas modern mainland Southeast Asians, including Cambodians, were more affected by gene flow from later migrants from East Asia into this region.