Many sea urchin species excavate pits in sedimentary rock, transforming primary rocky substrates into sea urchins' pits. These pits are not only used as their home but seem to harbor a distinct assemblage of organisms. We investigated small-scale spatial variation in community of macroinvertebrates by comparing community composition of epilithic macroinvertebrates between those found on unmodified rocky substrate, inside pits occupied by rock-boring sea urchin Stomopneustes variolaris (Lamarck, 1816), and unoccupied pits, on an intertidal rocky shore in southern Thailand. Size structures of macroinvertebrates were compared between pits and analyses were performed to investigate whether the use of habitat depends on availability of space, or biological interactions between sea urchins and other macroinvertebrates. Size structure of the most abundant mobile fauna, top shells Trochus radiatus Gmelin, 1791, were also analyzed to assess whether they exhibit ontogenetic changes in habitat use. Although a few species were found in all habitat types, community compositions were different. Chitons and limpets were found exclusively on unmodified substrate; whereas relatively large-sized gastropods inhabited unoccupied pits, and occupied pits harbored small-sized crustacean and gastropod species. Generally, in occupied pits, small-sized faunas were more abundant than larger faunas, suggesting that sea urchin's body may function as a biogenic structure providing refugia for small-sized individuals. In unoccupied pits volume of all macroinvertebrates increased as available space increased. This was not observed in occupied pits, where disturbances due to sea urchin's activities may be more important in determining habitat use.