Acanthurids (surgeonfishes) are an abundant and diverse group of herbivorous fishes on coral reefs. While their contribution to trophic linkages and dynamics in coral reef systems has received considerable attention, the role of linkages involving their parasites has not. As both consumers of fish tissue and prey to microcarnivores, external parasites may play a significant role in trophic transfer between primary consumers (and hence their predominantly algae-based diet) and the broader coral reef community. Stable isotope analysis is a common tool for studying trophic linkages which can be used for studies involving parasites. We examined the stable isotope ecology (13C and 15N) of copepod (Caligus atromaculatus) and monogenean (Neobenedenia sp.) ectoparasites collected from two species of Caribbean acanthurids (Acanthurus coeruleus and Acanthurus bahianus). There were significant intraspecific differences in isotope discrimination factors between parasites collected from the two different host species as well as interspecific differences between parasites collected from the same host species. Discrimination factors for 15N were consistently positive but varied in magnitude depending on host and parasite species and were slightly lower than what would be expected for consumers. The 13C discrimination factors for both monogeneans and copepods collected from A. coeruleus were consistently positive but were negative for copepods collected from A. bahianus. These findings emphasize the complexity of the stable isotope trophic interactions occurring between parasites and their hosts, highlighting the value of these types of host-parasite isotopic studies.