The geological and climatic history of the Mediterranean basin over the last 6 million years has been determinant in shaping current geographic distribution of genetic variation in organisms. Phylogeographical approaches are considered one of most useful analysis for unraveling the evolutionary history of species. The Helichrysum pendulum complex is a group of three closely related plant species distributed in several islands and isolated continental localities of the Western-Central Mediterranean basin, providing an ideal case of study to analyze the processes involved in modelling its current genetic structure. Two cpDNA region rpl32-trnL intergenic spacer and the nrDNA region ETS were sequenced for 1-8 individuals from each of the 44 total populations sampled, covering the whole geographic range of the complex. Our results suggest that the complex originated in northern Africa and colonized several islands and continental areas of the northern Basin through the Gibraltar and Sicilian straits during phases of low sea level, favored by long distance dispersal events. While ETS data suggest a model of isolation by distance and show a main genetic barrier between populations of Western and Central Mediterranean areas, the rpl32-trnL reveals the existence of two divergent and not geographically structured haplotype groups within the complex. Ancient hybridization events among lineages of sect. Stoechadina are suggested as the most plausible cause for the haplotypes pattern observed, while several evidences of current hybridization between H. pendulum and several species of sect. Stoechadina are also detected in ETS data.