Climatic and anthropogenic stressors have degraded coral reefs globally, causing the abundance and composition of reef-associated taxa to shift. However, it is unknown how coral reef degradation may influence the abundance and composition of coral reef parasite communities. This study investigated how different coral reef habitats, representing a gradient of coral reef health, influenced parasitism of the common damselfish, Pomacentrus wardi. Thirty P. wardi were collected from three habitats on each of three inshore reefs of the GBR and their parasite communities quantified. The proportion of P. wardi infected with ectoparasites was lower in macroalgae relative to rubble habitats and intermediate in coral habitats. Yet, there were no consistent differences in ectoparasite abundance among habitats. Higher abundances of endoparasites infected P. wardi in coral relative to macroalgae and rubble habitats, yet there were no differences in endoparasite prevalence or richness among habitats. Habitat differences in parasitism of P. wardi may reflect differences in the habitat requirements and life cycles of individual parasites, differences in parasite predation, or variable exposure to parasites among habitats. These findings highlight the importance of including parasitism and parasite communities in understanding how habitat degradation may affect the function of coral reef ecosystems into the future.