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Abstract Human societies are characterized by norms that restrict selfish behavior and promote cooperation. The oxytocin system is an important modulator of social behavior that may be involved in the evolution of cooperation. Oxytocin acts in both the nucleus accumbens and the anterior cingulate cortex to promote social bonding and social cohesion. Expression of theCD38andOXTRgenes is known to affect oxytocin secretion and binding, respectively, in these brain areas. The Andean highlands provide an excellent opportunity to evaluate the role of oxytocin in the evolution of cooperation. The rich archeological record spans 13,000 years of population growth and cooperative challenges through periods of highland exploration, hunting economies, agro‐pastoralism, and urbanization. Through allele trajectory modeling using both ancient and contemporary whole genomes, we find evidence for strong positive selection on theOXTRandCD38alleles linked with increased oxytocin signaling. These selection events commenced around 2.5 and 1.25 thousand years ago, placing them in the region's Upper Formative and Tiwanaku periods—a time of population growth, urbanization, and relatively low rates of violence. Along with remarkable and enduring cultural developments, increased oxytocin secretion and receptor binding in these brain areas may have facilitated large‐scale cooperation that promoted early urbanization in the Titicaca Basin of the Andean highlands.