Sequence data from the first hypervariable segment of the mitochondrial DNA control region of 124 subjects belonging to three African-Brazilian and three Brazilian Indian populations were compared with information related to 12 protein genetic loci from 601 persons living in the same localities. There is high diversity among the mtDNA sites, and the most variable in one ethnic group are not the most variable in the other. No differences in gene diversity between populations within ethnic groups were observed, but the Indians showed a reduced variability. Much more interpopulation variation was observed in the mtDNA data than in the protein set. The relationships obtained for the six populations, however, are the same regardless whether mtDNA or protein loci are considered. African-Brazilians from Porto Alegre and Salvador, situated 3,000 km apart, are more similar to each other than both are to Paredão, despite the geographical proximity between Porto Alegre and Paredão, which are just 50 km apart. The tree topology in relation to the three Indians groups, on the other hand, is that expected when languages, culture, and geography are considered.