Recent Quaternary geological and climate events have shaped the evolutionary histories of plant species in the Mediterranean basin, one of the most important hotspots of biodiversity. Genetic analyses of the western Mediterranean Cheirolophus intybaceus s.l. (Asteraceae) based on AFLP were conducted to establish the relationships between its close species and populations, to reconstruct the phylogeography of the group and to analyse potential unidirectional versus bidirectional dispersals between the Ibero-Provençal belt and the Balearic Islands. AFLP data revealed two main genetic groups, one constituted by the Balearic populations and Garraf (NE Iberia) and the other formed by the remaining mainland populations that were further sub-structured into two geographically separated subgroups (SE + E Iberia and NE Iberia + SW France). Genetic diversity and spatial structure analyses suggested a mid-Pleistocene scenario for the origin of C. intybaceus in southern Iberia, followed by dispersal to the north and a single colonisation event of the Balearic archipelago from the near Dianic NE Iberian area. This hypothesis was supported by paleogeographic data, which showed the existence of terrestrial connections between the continent and the islands during the Middle–Late Pleistocene marine regressions, whereas the more recent single back-colonisation of the mainland from Mallorca might be explained by several hypotheses, such as long-distance dispersal mediated by migratory marine birds or sea currents.