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The importance of surnames in genetic studies has been recognized for a century or so. While the ethnic affiliations of individuals are ordinarily established in genetic studies by admixture analysis based on gene frequencies, often there are implicit assumptions in these attempts that are difficult to validate in the absence of detailed ethnohistories. In northern Chile and western Bolivia, where genetic admixture has been known to occur among the Aymara Indians and Spanish Caucasoids, the naming pattern (parental patri- and matrinyms) allowed us to classify individuals on the basis of the frequency of Aymara names into 9 ‘ethnic’ groups. From a sample of 2525 individuals it is shown that admixture occurred in lineages nonrandomly, implying assortative mating of surnames. Admixture and genetic distance analysis on the basis of 31 genetic markers on approximately 1700 of these individuals reveals that there is a reasonable agreement of ethnic classification of individuals by name and phenotype data on genetic markers. The Aymara-named groups are shown to be predominantly Amerindian (89%) in their genetic profiles. Individuals whose current naming pattern is basically Spanish also exhibit a substantial fraction of genes of Amerindian origin (67%). Presence of some rare alleles not found in Amerindian or Spanish Caucasoids in the admixed groups suggest infiltration of Negroid genes in the past.