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Inferring the evolutionary history of Mediterranean plant lineages from current genetic, distributional and taxonomic patterns is complex because of a number of palaeoclimatic and geological interconnected factors together with landscape heterogeneity and human influence. Therefore, choosing spatially simplified systems as study groups is a suitable approach. An amplified fragment length polymorphism (AFLP) study using two restriction enzyme combinations (EcoRI/MseI and KpnI/MseI) was carried out to estimate the structure of genetic variation throughout the range of Armeria pungens. This species has a West Iberian‐Corso/Sardinian disjunct distribution on coastal sand‐dune ecosystems. Bayesian, amova and genetic distance analyses of the AFLP data revealed the same distinguishable genetic groups, which do not match the main geographical disjunction. Corso‐Sardinian populations were found to be …