Multiple factors related to complex geomorphological and climatic history, in addition to biological factors such as hybridization, hinder the definition of some Mediterranean plant groups. The existence of controversial taxonomic treatments, the possible hybridization events involved, and its unknown evolutionary history, make the Helichrysum pendulum complex of H. sect. Stoechadina an ideal model to understand general processes of Mediterranean plant systematics and evolution. The mosaic range of the complex, which is distributed over several islands and continental areas in the western-central Mediterranean Basin, provides an opportunity to investigate how past connections and disconnections between landmasses may have determined the current geographic distribution of genetic variation in this area. The cpDNA region rpl32-trnL intergenic spacer and the nrDNA region ETS were sequenced for 1–8 individuals from each of the 44 populations sampled, covering all taxa and the whole geographic range of the complex. These individuals were analysed together with a broad sampling of the remaining members of sect. Stoechadina. In addition, detailed multivariate analyses of morphological characters were performed for the whole section and for the H. pendulum complex. Considering together distinctive genetic and morphological traits, our species concept is presented and discussed in a context of integrative taxonomy, and five species are recognized within the complex: H. errerae, H. melitense, H. pendulum, H. saxatile and H. valentinum. The first three species are recognizable by qualitative and quantitative morphological traits, and are genetically distinguishable from the rest as shown by the molecular markers analysed. The two last species are reported here to have a putative ancient hybrid origin and are also genetically distinguishable from the rest but morphologically recognisable only by quantitative characters. Phylogenetic relationships shown by nuclear and chloroplast markers, and an intermediate morphology between the two putative parental taxa, point to H. pendulum and H. italicum as the putative parental taxa for H. saxatile, and H. pendulum and H. stoechas as putative parental taxa for H. valentinum. In a discriminant analysis of the five species, 97.8% of all individuals were classified correctly. The high level of haplotype and ribotype diversity observed in North Africa indicates that this region is either the area of origin of the complex or a secondary contact zone. Our results suggest that the complex colonized several islands and migrated through the Gibraltar and Sicilian Straits during phases of low sea level, favoured by local dispersal events that promoted its gradual range expansion. The occurrence of the complex in the Balearic Islands, which have remained isolated even during low sea level phases, could be explained by stochastic long-distance dispersal events.