Madagascar boasts a substantial radiation within Hibisceae (Malvaceae). Molecular data were used to determine the number of migrations to Madagascar, to clarify the timing of these radiations, and to assess the relationships among the endemic taxa. Sequences of matK and ndhF were obtained for representatives of all the Malagasy endemic genera in Hibisceae, as well as representative Malagasy species of Hibiscus and Kosteletzkya. Phylogenetic analysis of these data along with a sampling of outgroups and other major lineages of Hibisceae strongly supported the existence of an exclusively Malagasy clade, the /Megistohibiscus clade, which is sister to the rest of tribe Hibisceae. Humbertiella, Megistostegium, Perrierophytum, all the Malagasy Kosteletzkya, and a number of endemic species usually placed in Hibiscus are members of /Megistohibiscus and appear to be derived from a single introduction to Madagascar in the mid Miocene. Other sampled Malagasy Hibisceae, including the endemic genera Helicteropsis, Jumelleanthus, and Macrostelia, were resolved as members of the /Euhibiscus clade, implying at least one additional dispersal to the island.