Traditionally, pre-contact Native Americans have served as a biological reference for identifying modern Asian individuals in aspects of the biological profile due to their distantly shared genetic history, although this assumption remains largely untested. This study explores the craniomorphic variability between Asian and Asian-derived groups to ascertain whether they can be differentiated using population-specific models. Cranial and mandibular nonmetric trait data were recorded on pre-contact Native Americans (n=150) and compared within a statistical framework to cranial trait data for modern Thai (n=150) and Japanese (n=150) individuals. Chi-square analyses indicate that the groups exhibit statistically significant differences in their trait expressions. Of the 35 traits analyzed, 31 differ significantly between the groups. Binary logistic regression equations for differentiating the Japanese, Thai, and Native Americans are presented, and cross-validated correct classification rates range 60.0-90.0%. Further, the inclusion of sex into the logistic regression equations failed to improve their accuracies. The results indicate that the Native American and Asian groups are not skeletally homogenous due to divergent population histories, and that numerous cranial and mandibular nonmetric traits are resolute enough to detect differences within and between Asian and Asian-derived groups. Thus, this study highlights the utility of nonmetric traits in identifying individuals beyond the traditional African (“Black”), (“White”), and Asian groupings.