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Aim Studies of climate change impacts on animal distributions typically consider only the direct impacts of a changing climate, under the assumption that future areas of suitable climate will otherwise remain ecologically suitable. Here we assess both the direct and indirect impacts of climate change on rain forest ant communities, where substantial shifts are projected to occur for both climate and habitat types. Location Australian Wet Tropics (AWT). Methods Generalized Dissimilarity Modelling was used to model turnover in the composition of similar to 300 rain forest ant species sampled at 150 sites across six mountains spanning five degrees of latitude. Ants were sampled within the leaf litter, on the litter surface and on tree trunks. By modelling the rate of turnover among sites, we determined the current effective area of similar ecological environments (SEE) for ant communities and consequently the expected change in species persistence when habitat shifts under two climate projections for the years 2035, 2055 and 2085. We compared results when SEE considered only the direct effects of a changing climate, with those when changes in habitat were also included. Results The rain forest ant communities modelled will lose a substantial proportion of SEE under both climate change scenarios. Under combined direct (changes in climate) and indirect (changes in rain forest habitat) impacts of climate change, >90% of the communities in the region were predicted to lose up to half their similar habitats compared with 50%-60% when only considering direct climate change impacts. The highest risk of reduction in area of SEE is projected in drier inland areas of the AWT, where profound compositional turnover is linked to dramatic changes in rain forest vegetation, including extensive conversion into savanna. Main conclusions Our findings emphasize the importance of incorporating habitat suitability into future projections of species turnover under a changing climate, particularly for habitats where vegetation structure is projected to undergo profound change.