A total of 582 individuals (1,164 chromosomes) from two African, eight African‐derived South American, five South American Amerindian, and three Brazilian urban populations were studied at four variable number of tandem repeat (VNTR) and two short tandem repeat (STR) hypervariable loci. These two sets of loci did not show distinct allele profiles, which might be expected if different processes promoted their molecular differentiation. The two African groups showed little difference between them, and their intrapopulational variation was similar to those obtained in the African‐derived South American communities. The latter showed different degrees of interpopulation variability, despite the fact that they presented almost identical average degrees of non‐African admixture. The FST single locus estimates differed in the five sets of populations, probably due to genetic drift, indicating the need to consider population structure in the evaluation of their total variability. A high interpopulational diversity was found among Amerindian populations in relation to Brazilian African‐derived isolated communities. This is probably a consequence of the differences in the patterns of gene flow and genetic drift that each of these semi‐isolated groups experienced. Am J Phys Anthropol 109:425–437, 1999. © 1999 Wiley‐Liss, Inc.