How important are refugia for plankton biogeography? Here for the first time we report living cysts of the fossil dinoflagellate Dapsilidinium pastielsii from Southeast Asia: Shioya Bay (Okinawa, Japan), Koror (Palau), Ambon (Indonesia), East Vietnam Sea (Vietnam), and Masinloc (the Philippines). This species, thought to have become extinct in the early Pleistocene, is the last survivor of a major early Cenozoic lineage. Its disappearance from the Atlantic following the early Pleistocene implies cooling, and the discovery of living D. pastielsii in the Indo-Pacific warm pool suggests that this unique environment with stable temperatures served as an important refuge for thermophilic dinoflagellates with a >50 m.y. lineage. This is the first record of a refugium plankton species within the Indo-Pacific warm pool.