ABSTRACT1. Conservation managers require biodiversity assessment tools to estimate the impact of human activities on biodiversity and to prioritize resources for habitat protection or restoration. Large-scale programs have been developed for freshwater ecosystems which grade sites by comparing measured versus expected species richness. These models have been applied successfully to habitats that suffer from systemic pressures, such as poor water quality. However, pressures in other habitats, such as rocky intertidal shores, are known to induce more subtle changes in community composition.2. This paper tests a biodiversity assessment methodology that uses the ANOSIM R statistic to quantify the biological dissimilarity between a site being assessed and a series of reference sites selected on the basis of their similar environmental profile. Sites with high R values for assemblage composition have an anomalous assemblage for their environmental profile and are potentially disturbed.3. This methodology successfully identified moderate to heavily perturbed sites in a pilot study on 65 rocky intertidal sites in south-eastern Australia. In general, measures based on percentage cover (flora and sessile invertebrates) were more sensitive than abundance (fauna).