Anisopappus (Asteraceae: Athroismeae) is a genus with its main distribution in Africa (one species also in Asia), currently considered to include around 21 species. A molecular phylogenetic study of Anisopappus is presented for the first time, based on plastid (ndhF, trnL-trnF, trnQ-rps16) and nuclear (ETS, ITS) data. Anisopappus is confirmed to be monophyletic, and species interrelationships are resolved. The results differ from earlier treatments based on morphology, and the phylogenetic analyses reveal a need for changes in species circumscriptions as compared to those of the most recent treatment. Consequently, many taxa currently treated as synonyms are here shown to represent separate species indicating that the genus includes well over 40 species. Distribution patterns now emerge where several clades are found to consist of species restricted to a particular geographical region. The Anisopappus of Madagascar, many of which were earlier placed in synonymy with species found on the African continent, are here shown to be endemic, and the results reveal a need for further studies of that group.