Marine protected areas (MPAs) represent a potentially useful management tool to preserve biodiversity. Protection effectiveness was investigated at Tavolara-Capo Coda Cavallo MPA by comparing assemblages of rocky shores at a location A level of protection (island), with those at two locations at B level of protection (one on an island and one on the mainland coast) and two at C level of protection (one on an island and one on the mainland coast).Results did not indicate significant differences in structure of intertidal assemblages among locations under different levels of protection (A, B and C). Protection was not found to be a significant source of variation to low-shore assemblages investigated. In contrast, assemblages seemed to be more dependent on the geographical location within the MPA. Results have important implications for conservation of marine coastal assemblages and would indicate that inclusion of representative assemblages within systems of marine protected areas should target rocky shores both on the mainland and on islands.