This dataset gathers the names of 86 species of fish as well as their trophic category, abundance and biomass per replicate, sampled by bottom trawling in Posidonia oceanica beds in three main geographic areas (Marseille, Port-Cros Island and Galeria in Corsica) of the Mediterranean French coast. Samples were collected by bottom trawling performed in seagrass meadows between 10 and 40 m depth at different seasons (summer-winter) and period (day-night) at several occasions between 1980 and 2013. This dataset is a witness of the structure, functioning and evolution of fish assemblages in north-western Mediterranean Posidonia oceanica beds.