The densities of newly settled coral trout (Plectropomus leopardus, Pisces, Serranidae) were monitored in a variety of habitats on Green Reef in the Cairns section of the Great Barrier Reef to assess whether spatial patterns of recruitment are influenced by physical features of the substratum, and whether this species uses different habitats during its ontogeny. Surveys showed that small juveniles used sites that were significantly different from random and that these habitat associations changed as the fish grew larger. Specifically, coral trout recruited to level patches of rubble substrata >5 m2 and subsequently shifted to high relief features. Densities of recruits were related to the amount of rubble substrata available.