The distribution and density of Pinna nobilis was assessed along the eastern and southeastern coasts of Tunisia, based on line-transect data collected by SCUBA diving. An information-theory approach was followed for inference, and generalized additive models were fitted to model the population density of fan mussels using environmental and spatial covariates. The density of fan mussels was significantly correlated with depth and the distance from the city of Gabes. The fan mussel density was practically zero in very shallow water (<0.3 m depth) and increased with depth within the depth range of this study (0–6 m). The species was observed within Posidonia oceanica, Cymodocea nodosa and Caulerpa prolifera beds, with no evident difference in density among habitats. Zero fan mussel densities were observed near the city of Gabes. Population density increased with the distance from Gabes and was higher in the south than in the north. This decline of P. nobilis density near Gabes could be an effect of marine pollution due to the dumping of large quantities of phosphogypsum and other chemical products and the associated degradation of the benthic habitats in the area during recent decades.