Ptilostemon is a fine example of the representatives of the eastern groups of the Cardueae that have diversified in the western Mediterranean. Relationships to Cynara, which exhibits a similar distribution, and Lamyropsis, which is morphologically closer according to previous studies, are investigated using Bayesian analysis of DNA sequences of the plastid intergenic spacer ycf3-trnS and two nuclear regions, the ETS and ITS spacers. The sectional classification and biogeography of Ptilostemon are also revised in the light of the molecular phylogeny. Our results suggest that Cynara is the most plausible sister genus to Ptilostemon. Some paralogous copies of the ETS region found among species of the three genera by cloning are interpreted as incomplete lineage sorting of ancestral polymorphisms. The current sectional classification of Ptilostemon shows excessive fragmentation, which does not agree with our phylogeny, and therefore a more synthetic classification is proposed. The present distribution of Ptilostemon indicates that there were two colonization events in the western Mediterranean region, paralleling a similar pattern of successive waves already suggested for Cynara.