Abstract Genomic research in Latin America has looked into the African, Amerindian and European ancestry of local populations. This article explores how indigeneity and blackness figure in genomic science in the light of previous and current representations of indigenous and Afro-descendent people. These categories have been cast as ‘other’ in Latin America, but they have occupied different locations in ‘structures of alterity’. I look briefly at these similarities and differences in the colonial and republican periods and in recent multiculturalist reforms. I look at the gendered sexual imagery surrounding each concept, before examining in detail how blackness and indigeneity figure in gendered ways in genomic science research on admixture and ancestry in Brazil, Colombia and Mexico. I conclude that, in the context of multiculturalism, genomics works to re-centre imaginaries of the nation around the mestizo and mixture, while casting blackness and indigeneity, in sexualised and gendered ways, as different kinds of others.