Patterns of rocky reef fish assemblages (composition and relative abundance of species) were examined to provide data on the design of Marine Protected Areas (MPAs), which aim to protect these organisms. A hierarchical design was used to investigate changes in fish assemblages at scales of metres to kilometres along-shore, and among reef habitat types within two 10-km areas on the central coast of New South Wales, Australia. Influences of physical and biological attributes of a reef on assemblages of fish were also examined. The greatest variation in fish assemblages occurred at scales of 2-6 km along-shore. Eighty percent of species recorded were found within a 6-km section of coastline. The most predictable differences in assemblages were found between reef habitats (urchin-grazed barrens, Ecklonia forest and sponge habitat), and between depths. Marine Protected Areas should ideally incorporate all available habitats over the entire depth range at which they occur. This may require MPAs larger than 2-6 km, or multiple MPAs that have been specifically located to include these features, as representation of habitats was found to vary at scales of kilometres to tens of kilometres along shore.