This study explores the extent to which ontogenetic habitat shifts modify spatial patterns of fish established at settlement in the Moorea Island lagoon (French Polynesia). The lagoon of Moorea Island was divided into 12 habitat zones (i.e. coral seascapes), which were distinct in terms of depth, wave exposure, and substratum composition. Eighty-two species of recently settled juveniles were recorded from March to June 2001. Visual censuses documented changes in the distribution of juveniles of each species over time among the 12 habitats. Two patterns of juvenile habitat use were found among species. Firstly, some species settled and remained in the same habitat until the adoption of the adult habitats (i.e. recruitment; e.g. Chaetodon citrinellus, Halichoeres hortulanus, Rhinecanthus aculeatus). Secondly, others settled to several habitats and then disappeared from some habitats through differential mortality and/or post-settlement movement (e.g. 65–70 mm size class for Ctenochaetus striatus, 40–45 mm size class for Epinephelus merra, 50–55 mm size class for Scarus sordidus). A comparison of the spatial distribution of juveniles to that of adults (61 species recorded at both stages) illustrated four patterns of subsequent recruitment in habitat use: (1) an increase in the number of habitats used during the adult stage (e.g. H. hortulanus, Mulloidichthys flavolineatus); (2) a decrease in the number of habitats adults used compared to recently settled juveniles (e.g. Chrysiptera leucopoma, Stethojulis bandanensis); (3) the use of different habitat types (e.g. Acanthurus triostegus, Caranx melampygus); and (4) no change in habitat use (e.g. Naso litturatus, Stegastes nigricans). Of the 20 most abundant species recorded in Moorea lagoon, 12 species modified the spatial patterns established at settlement by an ontogenetic habitat shift.