Five centuries ago, the Hispanic Monarchy conquered the Mexica Empire and imposed the colonial regime. The colonization process that followed profoundly transformed the lives of millions of people and altered the demographic dynamics of Mesoamerica. To maintain the economic exploitation of the land, the colonizers subjugated the local population and enslaved thousands of people from sub-Saharan Africa. Today, Mexican women and men are descendants of the admixture between these populations—an asymmetric process of cultural integration and genetic mixing that is still ongoing, shaped by the deep social inequalities that emerged from the conquest and persist to this day. In this project, we study the imprint of colonization in the DNA of archaeological samples from Mexico. We analyze changes in the population’s genetic structure before and after the conquest, and track the evolution of Mesoamerican genetic diversity over time. In addition, we investigate how social inequalities tied to admixture shaped Mexico’s genetic structure. To do so, we examine the distribution of Mesoamerican, European, and sub-Saharan genetic ancestry in men and women throughout the colonization process. These analyses allow us to infer how social structure have shaped Mexico’s genetic profile over the past five centuries.