The origins of the highly endemic and partly very diverse fauna and flora of Madagascar were longtime unsolved and are still strongly disputed, although dispersalists are recently prevailing over advocates of Gondwanan vicariance. Madagascar has been separated from other continents and continental fragments since the Mesozoic, and the assumption of vicariance origins requires very old ages of the lineages involved. Herein I review the recent progress of knowledge on the molecular phylogenetic relationships of the amphibians, reptiles, and other non-flying vertebrates of Madagascar. Of 17 Malagasy clades for which relationships seem to be resolved with sufficient and unanimous support, the largest proportion have their sister-group in Africa, and very few show a general area cladogram consistent with the succession of events in the fragmentation of the supercontinent Gondwana. A survey of pairwise sequence divergences between 25 Malagasy lineages and their non-Malagasy relatives in the 16S and 12S rRNA genes resulted in values that in most cases were distinctly below the saturation plateaus of these genes. Multiple calibrations based on 34 largely independent data points indicate that such saturation would be strongly expected in the case of ages corresponding to the geographical isolation of Madagascar in the Jurassic and Cretaceous. A Cenozoic age for most Malagasy lineages is therefore most likely. Analysis of phylogenetic patterns of some taxa provides indications for a scenario in which the ancestors of the Malagasy clades first arrived by transmarine dispersal from Africa at the Malagasy west coast, and in a second step a subset of them underwent species-rich radiations into the rainforests.