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Habitat connectivity in coral-reef ecosystems partly depends on fish movements, and considerable effort has been made to understand their temporal and spatial patterns of habitat use. In the Caribbean, the schoolmaster, Lutjanus apodus, typically settle and grow up in mangroves and seagrass beds, migrating later to coral reefs. However, direct settlement on reefs, or permanent stay in mangroves, has also been observed in some localities, raising the question of whether schoolmasters could exhibit a wider repertoire of conditional, context-specific strategies. We investigated this issue in a new region, i.e., the Mesoamerican Reef System, based on parasite tagging. A total of 220 juvenile schoolmasters 1–2 yr old collected in estuarine mangroves, estuary sandy flats with marine influence, and reefs, in the region of Chetumal Bay were examined for metazoan parasites. This parasite fauna (36 taxa) significantly changed along the estuarine-marine gradient. The long-lived larvae of Contracaecum sp. type 2, Gorgorhynchoides bullocki, and Neoterranova sp. recruited very frequently in fish from estuarine mangroves. Infection patterns of these parasites suggested that (i) the fish collected in mangroves had settled and lived there until collection (1–2 years); (ii) the infected fish collected in sandy flats and reefs (a minimum of ca. 20% of the sample) had an estuarine origin. The digenean Hamacreadium mutabile had a clear marine affiliation and was never collected in estuarine fish. This suggests that ‘marine’ schoolmasters had not performed commuting excursions to estuarine waters, at least within the last months prior to collection. The small size of some fish infected with H. mutabile conforms to a direct settlement on reefs. In summary, the parasitological evidence provides mixed evidence of both habitat migration and residency of schoolmasters, also illustrating the potential of parasites to unveil patterns of habitat use by coral-reef fishes. Inglés