Tunisia has experienced a variety of human migrations that have modeled the myriad cultural groups inhabiting the area. Both Arabic and Berber‐speaking populations live in Tunisia. Berbers are commonly considered as in situ descendants of peoples who settled roughly in Palaeolithic times, and posterior demographic events such as the arrival of the Neolithic, the Arab migrations, and the expulsion of the “Moors” from Spain, had a strong cultural influence. Nonetheless, the genetic structure and the population relationships of the ethnic groups living in Tunisia have been poorly assessed. In order to gain insight into the paternal genetic landscape and population structure, more than 40 Y‐chromosome single nucleotide polymorphisms and 17 short tandem repeats were analyzed in five Tunisian ethnic groups (three Berber‐speaking isolates, one Andalusian, and one Cosmopolitan Arab). The most common lineage was the North African haplogroup E‐M81 (71%), being fixed in two Berber samples (Chenini–Douiret and Jradou), suggesting isolation and genetic drift. Differential levels of paternal gene flow from the Near East were detected in the Tunisian samples (J‐M267 lineage over 30%); however, no major sub‐Saharan African or European influence was found. This result contrasts with the high amount of sub‐Saharan and Eurasian maternal lineages previously described in Tunisia. Overall, our results reveal a certain genetic inter‐population diversity, especially among Berber groups, and sexual asymmetry, paternal lineages being mostly of autochthonous origin. In addition, Andalusians, who are supposed to be migrants from southern Spain, do not exhibit any substantial contribution of European lineages, suggesting a North African origin for this ethnic group. Am J Phys Anthropol, 2011. © 2011 Wiley‐Liss, Inc.