In the absence of detailed assessments of extinction risk, ecological specialisation is often used as a proxy of vulnerability to environmental disturbances and extinction risk. Numerous indices can be used to estimate specialisation; however, the utility of these different indices to predict vulnerability to future environmental change is unknown. Here we compare the performance of specialisation indices using coral-feeding butterflyfishes as a model group. Our aims were to 1) quantify the dietary preferences of three butterflyfish species across habitats with differing levels of resource availability; 2) investigate how estimates of dietary specialisation vary with the use of different specialisation indices; 3) determine which specialisation indices best inform predictions of vulnerability to environmental change; and 4) assess the utility of resource selection functions to inform predictions of vulnerability to environmental change. The relative level of dietary specialisation estimated for all three species varied when different specialisation indices were used, indicating that the choice of index can have a considerable impact upon estimates of specialisation. Specialisation indices that do not consider resource abundance may fail to distinguish species that primarily use common resources from species that actively target resources disproportionately more than they are available. Resource selection functions provided the greatest insights into the potential response of species to changes in resource availability. Examination of resource selection functions, in addition to specialisation indices, indicated that Chaetodon trifascialis was the most specialised feeder, with highly conserved dietary preferences across all sites, suggesting that this species is highly vulnerable to the impacts of climate-induced coral loss on reefs. Our results indicate that vulnerability assessments based on some specialisation indices may be misleading and the best estimates of dietary specialisation will be provided by indices which incorporate resource availability measures, as well as assessing responses of species to changes in resource availability.