A new study sheds light on the genetic events that shaped the population structure of South America. Homburger et al. analysed genome-wide single-nucleotide polymorphism (SNP) data to trace the European and Native American ancestral origins of admixed Latino individuals from five South American countries. Principal component analysis identified the Iberian Peninsula as the predominant source of European ancestry. The origins of Native American ancestral components differed between Latino populations, indicating that admixture between European colonists and Native American populations occurred across South America. Modelling based on ancestry tract length indicated that the initial admixture events occurred between 9 and 14 generations ago, and that a later burst of European migration to South America occurred between 3 and 9 generations ago. The heterogeneity revealed by this study demonstrates the importance of including diverse populations in genetic association studies.