High species diversity and endemism within Madagascar is mainly the result of species radiations following colonization from nearby continents or islands. Most of the endemic taxa are thought to be descendants of a single or small number of colonizers that arrived from Africa sometime during the Cenozoic and gave rise to highly diverse groups. This pattern is largely based on vertebrates and a small number of invertebrate groups. Knowledge of the evolutionary history of aquatic beetles on Madagascar is lacking, even though this species-rich group is often a dominant part of invertebrate freshwater communities in both standing and running water. Here we focus on large bodied diving beetles of the tribes Hydaticini and Cybistrini. Our aims with this study were to answer the following questions 1) How many colonization events does the present Malagasy fauna originate from? 2) Did any colonization event lead to a species radiation? 3) Where did the colonizers come from—Africa or Asia—and has there been any out-of-Madagascar event? 4) When did these events occur and were they concentrated to any particular time interval? Our results suggest that neither in Hydaticini nor in Cybistrini was there a single case of two or more endemic species forming a monophyletic group. The biogeographical analysis indicated different colonization histories for the two tribes. Cybistrini required at least eight separate colonization events, including the non-endemic species, all comparatively recent except the only lotic (running water) living Cybister operosus with an inferred colonization at 29 Ma. In Hydaticini the Madagascan endemics were spread out across the tree, often occupying basal positions in different species groups. The biogeographical analyses therefore postulated the very bold hypothesis of a Madagascan origin at a very deep basal node within Hydaticus and multiple out-of-Madagascar dispersal events. This hypothesis needs to be tested with equally intense taxon sampling of mainland Africa as for Madagascar.