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Madagascar is a complex 'biodiversity hotspot' with a rapidly dwindling biota. The Late Quaternary subfossil record includes many extinct species whose loss is attributed to natural climate change and human impacts. Investigation of the chronology of these events is challenging because few localities document pre-Holocene communities not impacted by humans. Caves with extinct lemurs of large body size comprise some of Madagascar's richest subfossil sites, but provide only a limited window into the island's past. Open highland sites may have fewer primates, but may better document other megafauna, and allow the analysis of the role of the Central Highlands as refugia and as corridors for the dispersal of vertebrates before and after human arrival. Here we present a new subfossil site, Tsaramody (Sambaina basin, Central Madagascar), a high-altitude wetland area that preserves a diverse late glacial and postglacial vertebrate community. Tsaramody bears testimony to fluctuations in the highland flora during the transition from glacial to postglacial conditions, and the composition of a highland vertebrate community before humans arrived. We compare its biota to those of other sites to begin to document the decline and disappearance of megafauna from some of Madagascar's open ecosystems - wetlands dominated by hippopotamuses and crocodylians.