Populations of generalist species often comprise of smaller sub-sets of relatively specialized individuals whose niches comprise small sub-sets of the overall population niche. Here, the role of parasite infections in trophic niche specialization was tested using five wild fish populations infected with the non-native parasite Ergasilus briani, a copepod parasite with a direct lifecycle that infects the gill tissues of fish hosts. Infected and uninfected fishes were sampled from the same habitats during sampling events. Prevalence in the host populations ranged between 16 and 67%, with parasite abundances of up to 66 parasites per fish. Although pathological impacts included hyperplasia and localized haemorrhaging of gill tissues, there were no significant differences in the length, weight and condition of infected and uninfected fishes. Stable isotope analyses (δ13C, δ15N) revealed that the trophic niche of infected fishes, measured as standard ellipse area (i.e. the isotopic niche), was consistently and significantly smaller compared with uninfected conspecifics. These niches of infected fishes always sat within that of uninfected fish, suggesting trophic specialization in hosts. These results suggested trophic specialization is a potentially important non-lethal consequence of parasite infection that results from impaired functional traits of the host.