Mayapan was the largest and most densely populated city in the Maya area during the Late Postclassic period (ca. AD 1200–1450), but was it truly cosmopolitan? This question was investigated through biodistance and population genetic analyses of heritable dental metric traits, the first such study conducted at this site. The analyses concentrated on burials excavated from a diverse array of contexts, such as mass graves, residences, and plaza floors, with a particular focus on freestanding shrine ossuaries. The results of both univariate and multivariate analyses suggest individuals interred in freestanding shrine ossuaries are genetically distinct from contemporary and earlier populations from northwestern Yucatan, suggesting this new burial practice was introduced by foreigners. These findings also have implications for the larger question of whether pan-Mesoamerican elite identity formation in the Postclassic period (AD 900–1543) was accompanied by more intense long-distance mixing of populations, rather than just the exchange of goods and ideas. Given the important role played by exchange in the regeneration of sociopolitical complexity in ancient societies from different parts of the world (Schwartz, 2006), this study also contributes to the broader discussion of how cultures survive and respond to upheaval, as well as to a more nuanced consideration of the role of migration in culture change.