The temporal origin of Madagascar's extraordinary endemic diversity is debated. A preference for Cenozoic dispersal origins has replaced the classical view of Mesozoic vicariance in the wake of molecular dating. However, evidence of ancient origins is mounting from arthropod groups. Using phylogenetic 'tip-dating' analysis with fossils, we show that a whirligig beetle species, Heterogyrus milloti, inhabiting forest streams in southeastern Madagascar is the last survivor of a once dominant and widespread Mesozoic group. With a Late Triassic to Early Jurassic origin (226-187 Ma) it is the hitherto oldest dated endemic lineage of animal or plant on Madagascar. Island biotas' sensitivity to extinction is well known, but islands can also provide refuge from continental extinction. Heterogyrus milloti is an irreplaceable link to the freshwater biota of the Mesozoic and serves as a reminder of what may be lost without critical conservation efforts on Madagascar.