Abstract: Several issues regarding the extent of genetic variation in the cork oak (Quercus suberL.), and the evolutionary forces that shaped its biogeography are still unknown and controversial.New insights to infer intra-specific phylogeographic relationships in the previously neglectedNorth African cork oak stands are here provided by means of genetic analyses of the maternallyinherited plastid genomes (PCR-RFLP at 5 chloroplast loci). We have analysed 17 populationsfrom Morocco (7), Algeria (6) and Tunisia (4); resulting data were included in aphylogeographical framework obtained from 95 populations throughout the species range. Fivetotal haplotype lineages were identified for the entire species’ range. Of these, three haplotypesoccur along the North African Mediterranean coast, delineating two clear suture zones: at East(Northeastern Algeria) and at West (Central Morocco). Genetic diversity parameters weredetermined for the different geographic areas of the entire species range, showing interestingvariation where paleogeography, hybridization, adaptation, fragmentation, and human impact allplay an important role.The importance of the North African territories for the evolutionary history of the speciesand the urgency for measures to preserve the current biodiversity in this area are stressed.