Primula allionii is endemic to a tiny area of the Maritime Alps and has one of the narrowest distribution ranges in this hotspot of biodiversity. Phylogeographical patterns in P. allionii were studied using plastid DNA markers and dominantly inherited markers (AFLP and ISSR) to verify any admixture between P. allionii and the sympatric P. marginata and to detect the phylogeographical history of the species. Morphometric measurements of flowers and admixture analysis support the hypothesis that hybridization occurs in nature. Species distribution models using two climate models (CCSM and MIROC) suggested a reduction in habitat suitability during cold periods. Phylogeographical analysis suggested an old allopatric divergence during the mid-Pleistocene transition (about 0.8 Mya) without recolonization/contraction cycles. The Alps watershed does not act as a strong barrier between the two main areas of the distribution range, and moderate gene flow by pollen seems to create the admixture recorded among the stands. According to our results, the persistence of P. allionii throughout the Ice Age appears to be linked to the capacity of the Maritime Alps to provide a wide diversity of microhabitats consistent with the recent biogeographical pattern proposed for the Mediterranean Basin. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173, 637–653.