Abstract Patterns of distribution of reef fishes were examined across three spatial scales and related to habitat traits along 25 km of the northern Portuguese coast. Response variables included the multivariate assemblage structure, the total number of taxa and individuals, and the abundance of single groups categorized according to their preference for the benthic, proximo-benthic or pelagic environment, feeding and reproductive behaviour. Habitat traits included topographic elements (small and large 'drops' like cracks and crevices) and the extent of dominant morpho-functional types of macroalgae (kelp, large foliose, small erect, turf-forming filamentous, and encrusting). All fish responses were characterized by the largest variance at the smallest scale (among transects tens m apart), followed by that among reefs (hundreds m to 1 km apart) and almost null variance among sites (some km apart). Small and large 'drops' of the substratum explained, respectively, considerable variation of assemblage structure and the total abundance of individuals, while the extent of bare rock influenced the richness of taxa and that of benthic fishes, fishes feeding on sessile invertebrates and fishes laying benthic eggs or having nesting behaviour. Combinations of abiotic and biotic structural attributes of reefs influenced proximo-benthic fishes, the predators of mobile animals and fishes releasing pelagic eggs. The here reported associations between patterns of distribution of reef fishes and habitat traits have implications for the design of future protection schemes suitable to guarantee the conservation of reef fish communities and of the processes responsible for their variation. Within the SLOSS (single-large vs. several-small) debate in the design of marine reserves, for example, effective protection to the studied reef fishes would be provided by a set of small reserves, rather than a single large which might be appropriate for fishes having wider home ranges
