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 re-inscribes “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.