The incidence, distribution and infestation sequences of four endolithic cyanobacteria in the shells of the brown mussel Perna perna (L.) were studied along the south coast of South Africa. The incidence of endolith-infested shells varied significantly among the 21 study sites (∼23 to 95%), with highest infestation rates occurring on promontories and headlands as compared to sites within bays. At a smaller scale, the incidence of infested shells also varied with tidal height, being high at the upper tidal levels of mussel distribution and low or absent on the lowshore. The observation that small-scale variability in infestation rates was positively related to water movement suggested that physical damage to the outer protective periostracum of mussels may have facilitated colonisation by endoliths. This hypothesis was supported by the fact that shells with artificially damaged periostraca became infested at a greater rate than did control shells. Once colonisation by the filamentous cyanobacteria Plectonema terebrans, Hyella caespitosa and Mastigocoleus testarum had taken place, endoliths spread throughout the shell, causing progressive shell deformation and damage. Only older shells that were infested by the late successional, cavity-forming Pleurocapsa sp., however, exhibited severe shell deformations, became brittle and eventually fractured near the structurally important site of adductor muscle attachment. Heterotrophic endoliths typically associated with shell degradation in previous studies were extremely rare and if present did not contribute to shell disintegration. Although it is generally perceived that endolithic algae and cyanobacteria are restricted to the surface layers of shells by light limitation within the substratum, it is clear from this study that the interaction of a combination of factors (i.e. erosion of the periostracum, successional sequence of colonists and mechanical properties of the shell) may result in phototrophic endoliths causing severe shell degradation and eventually mussel mortality.