Habitat loss and climate change are major threats to amphibian species worldwide. We combined niche modelling under various climatic scenarios with analysis of habitat loss and the appropriateness of Cuban protected areas to identify major risk zones for the Endangered Cuban toad Peltophryne longinasus. Four subspecies with disjunct distributions associated with mountain forests are recognized. Our results suggest that the western subspecies, P. longinasus longinasus and P. longinasus cajalbanensis, are at risk from global warming, habitat degradation and potential additive effects. Peltophryne longinasus dunni, in central Cuba, has the lowest threat level related to climate change and habitat loss but could become increasingly threatened by the presence of the infectious disease chytridiomycosis. The eastern subspecies, P. longinasus ramsdeni, faces moderate impacts of climate change and habitat loss; however, low opportunity of migration to new areas and population decline justify a high threatened status for this subspecies. Our results predict minor temperature increases and precipitation decreases in the future. Nevertheless, at the biological level these changes could generate variations in species physiology, vocal behaviour and prey availability, and could probably increase the risk of predation. In Cuba protected areas have contributed to avoiding excessive forest loss but the potential impact of climate change was not considered in their original design. Our findings confirm that all subspecies of P. longinasus are threatened but management measures should be tailored according to the various predicted impacts.