Human population genomics aims to improve health for all, trace human migration histories and refine forensic identification techniques. These aims transcend national borders: geneticists are part of a global community supported by transnational infrastructures. At this level, concerns have been raised that, in its intense focus on genetic difference, genomics reinscribes “racial” differences. But global genomics is always enacted in specific contexts: although many projects are internationally collaborative, geneticists are embedded in national contexts and their data speak to questions of national identity and ethnic/”racial” diversity. In genomics in Brazil and Mexico “racial” difference is very clear – despite disavowals – because of the role of ideas about race mixture in national identity. Drawing on data collected in a comparative project, I show how genomic data figured in different ways in narratives about the Brazilian and Mexican nations. These national contexts show how “race” is reproduced in genomics more widely.