Human genetic structure of Iberian populations has been thoroughly explored in the last decades. The internal diversity of the Iberian Peninsula becomes visible by the different phylogeographic origins of particular mitochondrial DNA and Y chromosome lineages, which show a high degree of population specificity. In the present study, we combined information on matrilineal and patrilineal variation patterns in two autochthonous populations from Andalusia region (southern Spain). A special focus is made to a male sample set where both uniparental data is available. Gene diversities estimates yielded not statistical significant differences between both types of samples and markers. Genetic ancestry among Andalusians seems to be constituted by three foremost continental origins: European, African and Middle Eastern. The examined male group has revealed a noticeable proportion of individuals (over 45%) with a non-correspondence between maternal and paternal haplogroup origins, a signal of different population demographic histories linked to both sexes in the past. Andalusian males seem to be well differentiated according to ancestries. As expected, mtDNA diversity was much higher than that for Y chromosome, a fact that can be caused by patrilocality, which lead to particular social structures with effects on haploid genomes in modern human populations.