The decline of important coastal habitats, like seagrass meadows, is likely to influence populations of associated species, like the noble pen shell, Pinna nobilis. Here we used a Bayesian formulation of individual covariate models to derive a reliable estimate of populations of P. nobilis in shallow, and thus usually most impacted, areas around the island of Majorca, Balearic Islands, Spain. At six evaluated sites we find quite distinct densities ranging from 1.4 to 10.0 individuals/100 m2. These differences in density could not be explained by habitat factors like shoot density and meadow cover, nor did dislodgement by storms (evaluated by maximum wind speeds at the sites) seem to play an important role. However, noble pen shell density was related to anchoring as at sites where anchoring was not permitted the average density was 7.9 individuals/100 m2 while in sites where ships anchored the density was on average 1.7 individuals/ 100 m2. As for the conservation of Posidonia oceanica meadows, for the associated population of P. nobilis it would be of utmost importance to reduce anchoring pressure as a conservation measure for these endangered and protected bivalves.