Reef cryptofauna (animals inhabiting cracks and crevices) represent much of a reef’s biodiversity yet are seldom studied owing to their inaccessibility. Subtidal rocky reefs off Brunswick Heads and Byron Bay in northern New South Wales, Australia support benthic communities ranging from coral-dominated offshore reefs to kelp beds of Ecklonia radiata on inshore reefs. It was hypothesised that differential exposure to river discharge and the East Australian Current, as well as proximity to other reef habitats, may produce differences in recruitment and persistence of cryptofauna between superficially similar reefs within a small geographical range. Artificial crevice habitats were deployed at similar depths on three inshore reefs supporting similar Ecklonia densities. Although the species richness of crevice fauna was similar at all reefs, the species composition differed significantly along with the assemblages recruited in different seasons and to different crevice sizes. Neither reef faunas nor that of varying crevice sizes changed consistently with the seasons, yet all crevices appeared equally accessible to colonists. These results demonstrate the potential inadequacy of classifying reef communities for management of regional biodiversity based on the visual dominance of a few species that may not be as sensitive to environmental variables as many of the less obvious taxa.