Coral reef ecosystems provide important natural services to developing world societies, but are expected to show significant declines in species diversity, shifts in community composition and declines in productivity under climate change, increasing vulnerability of dependent societies to external shocks. Given current climate trajectories, adapting to these changes is an important goal for developing world societies and developing means of measuring changes in the functioning of coral reef ecosystems. Resilience is defined as the ability for an ecosystem to return to its original state of functioning following some external impact and can be represented by species diversity, particularly in ecosystems exposed to medium to high levels of disturbance, such as coral reefs, where high diversity plays an important role in maintaining ecosystem functioning. Here, we used species distribution models to produce projected changes in the species diversity of coral reef ecosystems in the ecologically distinct Caribbean large marine ecosystem, a socially and ecologically vulnerable region. The results of this study can provide a basis for the development of climate-proof policies for resource management and further explorations of resilience as a measure of ecosystem integrity.