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Identification of refugia from climate change is increasingly considered important for biodiversity conservation, but the distribution of putative refugia may vary across alternative climate scenarios, impeding conservation decision-making. Based on 117 plant species representative of ecoregions within south-eastern Australia, we provide a case study identifying in situ refugia across a spectrum of plausible future climates. We define in situ refugia as areas that currently contain populations of the target species, and are projected to remain climatically suitable in the future. Refugia were identified across scenarios describing futures that are, relative to 1990-2009, warmer and wetter, warmer/drier, hotter/wetter, and hotter with little precipitation change. Despite substantial variation in the spatial extent and longevity of climate refugia across species, ecoregions and climate scenarios, clear patterns emerged. By 2070, refugia for species in 1) deserts and xeric shrublands; 2) mediterranean forests, woodlands and shrublands; and 3) temperate and tropical grasslands are likely to be least extensive under a hotter/wetter future. Conversely, wetter conditions may lead to broader refugia for species in temperate forests. We identified areas of congruence where high richness refugia (refugia for >= 50% of representative species) were projected to occur irrespective of the climate scenario. These regions therefore appear robust to uncertainty about climate change, presenting clear targets for conservation attention. Our approach provides valuable information for decision-makers, enabling them to identify and visualise the spatial arrangement of refugia under contrasting scenarios of environmental change. This reveals management options in the context of climate uncertainty and facilitates informed prioritisation of conservation resources.