Population of Pedroches Valley, a hypothetical Berber settlement, located in the northwest portion of Córdoba province (Andalusia, Spain), had been analyzed for its Y-chromosome diversity. Moreover, to contextualize this population, 127 Y-chromosomes from a general Andalusia sample and a North African Berber community (Marrakech, Morocco) were also typed. For all samples, 24 single nucleotide polymorphisms of the non-recombining portion of the Y-chromosome (NRY) were analyzed and those samples described as belonging to E3b1b-M81 haplogroup were also typed for 16 Y-chromosome short tandem repeats. Our Analysis showed low levels of North African E3b1b-M81 haplogroup in the Pedroches Valley population (1.5%), which is a lower contribution than would be expected. This result rejects the hypothesis of a gradual genetic assimilation of Berber settlers during the Islamic period. © 2009 Wiley-Liss, Inc.