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North Africa is a crucial area in the settlement history of modern humans because it represents a possible connection between Africa and Europe. So far, genetic data were inconclusive about the fact that this region constitutes a barrier to gene flow, as previous results were highly variable depending on the genetic locus studied. The present study evaluates the impact of North Africa in reducing gene flow between populations from Africa and Europe, by comparing formally various genetic loci in the Y chromosome and analyzing several parameters of population differentiation taking into account the effects of both demography and natural selection at some loci. The Y chromosome is inherited through the paternal line and remains virtually unchanged through many generations. The combination of the analysis of Y chromosome STR and SNP will allow the analysis of human evolution in paternal lineages in different time scales. The forensic implication of the results are discussed.