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Brazil's Araucaria tree (Araucaria angustifolia) is an iconic living fossil and a defining element of the Atlantic Forest global biodiversity hotspot. But despite more than two millennia as a cultural icon in southern Brazil, Araucaria is on the brink of extinction, having lost 97% of its extent to 20th‐century logging. Although logging is now illegal, 21st‐century climate change constitutes a new—but so far unevaluated—threat to Araucaria's future survival. We use a robust ensemble modelling approach, using recently developed climate data, high‐resolution topography and fine‐scale vegetation maps, to predict the species' response to climate change and its implications for conservation on meso‐ and microclimate scales. We show that climate‐only models predict the total disappearance of Araucaria's most suitable habitat by 2070, but incorporating topographic effects allows potential highland microrefugia to be identified. The legacy of 20th‐century destruction is evident—more than a third of these likely holdouts have already lost their natural vegetation—and 21st‐century climate change will leave just 3.5% of remnant forest and 28.4% of highland grasslands suitable for Araucaria. Existing protected areas cover only 2.5% of the surviving microrefugia for this culturally important species, and none occur in any designated indigenous territory. Our results suggest that anthropogenic climate change is likely to commit Araucaria to a second consecutive century of significant losses, but targeted interventions could help ensure its survival in the wild. [ABSTRACT FROM AUTHOR]