Many reef-associated fishes initially recruit into mangroves, shifting outward to reefs as they grow and mature. Each ontogenetic habitat shift potentially exposes migrants to previously unencountered parasite taxa, likely increasing parasite species richness and driving changes in parasite community structure. However, studies on this topic rarely attempt to distinguish between the effects of habitat shifts versus a simple increase in individual fish size. We contrasted parasite community structure in Great Barracuda Sphyraena barracuda (N=77), Atlantic Needlefish Strongylura marina (N=49), Crevalle Jack Caranx hippos (N=57), White Mullet Mugil curema (N=75), and Yellowfin Mojarra Gerres cinnerus (N=54) from mangrove, inshore, and offshore habitats. Mullet harbored the highest observed parasite species richness (S=23, mean S=2.6±1.9) and Needlefish the lowest (S=6, mean S=0.4±0.8). GLM indicated that mean S differed significantly among habitats for Crevalle Jacks and Mullets, increasing with sequential habitat shifts; no significant effects were noted for fish size. PERMANOVA on (square root-transformed) Bray-Curtis similarity matrices found that both habitat shift and size significantly structured parasite communities for all fishes except Barracuda, with habitat shift (2.7>pseudo-F>25.9) playing a stronger role than size (2.0>pseudo-F>2.9). Our results suggest that ontogenetic habitat shifts are an important driver of parasite community composition and structure in these fishes.