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The origin of the contribution of uniparental heritage were analyzed in 615 samples of individuals proceeding from 13 towns classified according to historic differences in their emergence and development as African-derived, European-derived, and admixed/urban. Mitochondrial and Y-chromosome haplogroups were identified by PCR-restriction fragment length polymorphism. The results were compared with previous estimates of admixture made with autosomal markers and with historic aspects. The results show a predominantly indigenous genetic contribution through the female, being more prevalent in urban populations; the African contribution, although dispersed, presents a larger concentration in the African-derived towns, whereas the European contribution is limited to populations with this origin, reflecting isolation and the conservation of the distribution pattern of genes of the Colonial era. With regard to admixture through males, it is almost exclusively of European origin, whereas the African contribution is basically concentrated in the African-derived towns, and the Amerindian lineages are almost nonexistent. The genome of paternal heredity, as opposed to the autosomal and the mitochondrial, shows a homogeneous pattern of admixture that is independent of the origin of the population studied, suggesting that European genes have been introduced into the Venezuelan population through male immigrations, whereas the indigenous contribution has been preserved in the Venezuelan genetic pool through the women. These results provide evidence of the heterogeneity in the genetic origin of the Venezuelan population, which should be taken into account in forensic and epidemiologic genetic studies.