Stable isotopes of carbon and nitrogen characterize trophic relationships in predator–prey relationships, with clear differences between consumer and diet (discrimination factor Δ¹³C and Δ¹⁵N). However, parasite–host isotopic relationships remain unclear, with Δ¹³C and Δ¹⁵N remaining incompletely characterized, especially for helminths. In this study, we used stable isotopes to determine discrimination factors for 13 parasite–host pairings of helminths in coral reef fish. Differences in Δ¹⁵N values grouped according to parasite groups and habitat within the host with positive Δ¹⁵N values observed for trematodes and nematodes from the digestive tract and variable Δ¹⁵N values observed for cestodes and nematodes from the general cavity. Furthermore, Δ¹³C values showed more complex patterns with no effect of parasite group or habitat within host. Anegative relationship was observed between Δ¹⁵N and host δ ¹⁵N values among different host-parasite pairings as well as within 7 out of the 13 pairings, indicating that host metabolic processing affects host-parasite discrimination values. In contrast, no relationships were observed for Δ¹³C values. Our results indicate thatparasite group, habitat within host, and host stable isotope value drive Δ¹⁵N of helminths in coral reef fish while their effect on Δ ¹³C is more idiosyncratic. These results call for use of taxon- or species-specific and scaled framework for bulk stable isotopes in the trophic ecology of parasites.