Stable isotopes of carbon and nitrogen characterize trophic relationships in predator-prey relationships, with clear differences between consumer and diet (discrimination factor, Δ 13 C, Δ 15 N). However, parasite-host isotopic relationships remain unclear, with Δ 13 C and Δ 15 N 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. Δ 15 N differences grouped according to phylogeny and attachment site on the hosts: Δ 15 N was positive for trematodes and nematodes from the digestive tract and varied for cestodes and nematodes from the general cavity. Δ 13 C showed more complex patterns with no effect of phylogeny or attachment site. A negative relationship was observed between Δ 15 N and host δ 15 N value among different host-parasite pairings as well as within 7 out of the 13 parings, indicating that host metabolic processing affects host-parasite discrimination values. In contrast, no relationships were observed for Δ 13 C. Our results indicate that host phylogeny, attachment site and host stable isotope value drive Δ 15 N of helminths in coral reef fish while Δ 13 C 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.