Amphibians are thought to be unable to disperse over ocean barriers because they do not tolerate the osmotic stress of salt water. Their distribution patterns have therefore generally been explained by vicariance biogeography. Here, we present compelling evidence for overseas dispersal of frogs in the Indian Ocean region based on the discovery of two endemic species on Mayotte. This island belongs to the Comoro archipelago, which is entirely volcanic and surrounded by sea depths of more than 3500 m. This constitutes the first observation of endemic amphibians on oceanic islands that did not have any past physical contact to other land masses. The two species of frogs had previously been thought to be non-endemic and introduced from Madagascar, but clearly represent new species based on their morphological and genetic differentiation. They belong to the genera Mantidactylus and Boophis in the family Mantellidae that is otherwise restricted to Madagascar, and are distinguished by morphology and mitochondrial and nuclear DNA sequences from mantellid species occurring in Madagascar. This discovery permits us to update and test molecular clocks for frogs distributed in this region. The new calibrations are in agreement with previous rate estimates and indicate two further Cenozoic transmarine dispersal events that had previously been interpreted as vicariance: hyperoliid frogs from Africa to Madagascar (Heterixalus) and from Madagascar to the Seychelles islands (Tachycnemis). Our results provide the strongest evidence so far that overseas dispersal of amphibians exists and is no rare exception, although vicariance certainly retains much of its importance in explaining amphibian biogeography.