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Nine Atlantic islands with approximately five and a half centuries of demographic history constitute the Portuguese archipelago of the Azores. Despite the recent peopling history of these islands, written records regarding the specific origin and relative proportions of the first settlers are scarce and incomplete. To gain insights into the history of the peopling of the Azores and to evaluate to what extent population imports described in historical sources left their marks on the genetic constitution of the present-day populations, we analyzed 11 Y-chromosome biallelic markers in a sample of 145 unrelated individuals of Azorean ancestry. The main results of this study indicate that the genetic profile of the Azorean male population shows high affinities with that of mainland Portugal, in accordance with the general knowledge, derived from historical sources, that the Portuguese were the major contributors to the Azorean founding population. Nevertheless, genetic traces of settlers from other origins also mentioned in historical records can still be found in the present-day population. Thus typically sub-Saharan male lineages were detected in the archipelago, in contrast to what has been described for mainland Portugal. Furthermore, compared to what has been described for the mainland Portugal population, our data support a stronger influence of people of Jewish origin, as detected by an increased frequency of lineages belonging to haplogroup J.