Pinna nobilis is an endemic bivalve of the Mediterranean Sea. In the last decades P. nobilis populations have declined drastically due to increasing anthropogenic pressure and it has been declared a protected species since 1992. Despite the need for conservation, knowledge of the ecology and monitoring of the main populations of P. nobilis are limited. This study considered a population living within a Posidonia oceanica meadow in the Gulf of Oristano (western Mediterranean, Italy). The study area, about 150 hectares, part of which is included within a Marine Protected Area and a Site of Community Importance, was subdivided in 3 sub-areas. The percentage cover of different habitat types (P. oceanica, dead matte and sand) in each sub-area was measured and meadow features (substrate coverage, matte compactness and shoot density) characterized. The hypotheses of differences in density, percentage of dead individuals, population structure, shell burial level and orientation of P. nobilis, were investigated according to sub-areas and to habitat type. The spatial distribution was patchy, and the habitat type resulted a key factor in determining both density and distribution. A strong edge effect was demonstrated: more than half of the observed individuals colonized the P. oceanica border. Matte compactness and shoot density were found to affect the density and distribution of P. nobilis. Shell burial level and percentage of dead individuals varied with sub-areas and habitat types. Size distribution was bimodal and common shell orientation was observed in two sub-areas. These results contribute to increase the knowledge of population ecology of this species and to provide useful information for implementing conservation policies.