Chiliadenus is a small genus in the Inuleae (Asteraceae), consisting of ten species with allopatric distributions along the southern edge of the Mediterranean Sea. The different species have restricted areas of distribution, with only one being more widely distributed. The first molecular phylogenetic study of the genus with complete sampling, as well as a biogeographic analysis of the origin and biogeographic patterns leading to the current diversity of Chiliadenus is presented. Results confirm Chiliadenus as monophyletic and placed as sister to Dittrichia. The ancestor of Chiliadenus is dated to have diverged from that of Dittrichia around 5.45 Ma ago, coinciding with the Messinian salinity crisis, whereas the Chiliadenus crown group is dated to 2.29 Ma, around 3 million years later. Ancestral area reconstructions show the crown group to likely have originated in the area around Morocco and northwestern Algeria, which is also the area where the early divergences have occurred. Chiliadenus has then later diverged and dispersed over the Mediterranean to its current distribution. The evolution of the Chiliadenus crown group coincides with the onset of the Mediterranean climate, and its evolution may be connected to the subsequent climatic changes.