The Southwest United States (US) and Mesoamerica are often thought of as disparate regional networks separated by Northern Mexico. Chaco Canyon in the Southwest US, Tlatelolco in Central Mexico and Casas Grandes in Northern Mexico, all had large inter‐regional trade centres that economically connected these networks. This study investigated how factors such as geographic distance, shared migration history, trade and political interaction affected biological relationships and population affinities among sites in Mexico and in Southwest US during the Postclassic period (ad 900 ~ 1520). Distances based on cultural and geographic variables derived from archaeological and ethnohistoric data were compared with phenetic distances obtained from dental morphological traits. The results of Mantel tests show trade (corr = 0.441, p = 0.005), shared migration history (corr = 0.496, p = 0.004) and geographic distance (corr = 0.304, p = 0.02) are significantly correlated with phenetic distances, whereas political interaction (corr = 0.157, p = 0.133) is not. Partial Mantel tests show trade (corr = 0.223, p = 0.049) and shared migration history (corr = 0.493, p = 0.003) remain significant when controlling for similarities with geographic distance, although the correlation for trade and phenetic distance is lowered. Geographic distance is not significant when similarities with trade (corr = 0.067, p = 0.681) and shared migration history (corr = 0.148, p = 0.127) are controlled. These results highlight the importance of economic relationships and shared migration history across geographic regions in interpreting biological relationships among contemporaneous populations in prehistoric Mexico and the Southwest US. Copyright © 2013 John Wiley & Sons, Ltd.