The endemic Mediterranean seagrass Posidonia oceanica (L.) Delile forms meadows of great ecological importance that are presently under elevated anthropogenic pressures. In this study, a model of citizens’ observatory has been translated into practice to observe and monitor the health status of the Site of Community Importance, the Posidonia oceanica meadow named San Vito-Barletta extending along the coast of Apulia region in the Italian Southern Adriatic Sea. This meadow has been lately classified as “disturbed”. With the goal of gathering relevant data for the management and conservation of this meadow, we conducted underwater visual census of the epiphytes on P. oceanica leaves. Complementarily, population genetics analysis using highly variable microsatellites markers was carried out. Two campaigns of surveys in three different stations (Molfetta, Giovinazzo and Mola di Bari) revealed that the distribution of the epiphytic communities was not uniform among the meadow. In Molfetta station, the leaf-epiphytes biomass was visibly more abundant with increased filamentous epiphytes. The genetic analysis revealed that the San Vito-Barletta meadow shows an excess of heterozygosity and demonstrated the existence of at least two subpopulations. Since the sampling areas are situated along the coasts of different Apulian cities, this situation may reflect the diverse anthropogenic factors that vary from city to city. Therefore, as local citizens’ observatory, we now have to undertake the necessary actions to raise general public awareness of the need of this species protection at Apulian level and to promote good conservation practices before the meadow regresses irreversibly.