The deep shoal of Punta del Faro (Ligurian Sea, Mediterranean Sea) is a mesophotic rocky elevation hosting complex animal forests threatened by fishing activities. To identify appropriate conservation measures and set a reference example for similar cases, we present a detailed characterization of its megabenthic communities and a quantification of the fishing pressure. The results highlight the high natural value of the area, presenting high biodiversity (111 megabenthic and demersal species) and diverse types of animal forest, predominantly dominated by cnidarians. The tridimensional seascape is among the most complex in the eastern Ligurian Sea, but the long-term evaluation of its environmental status suggested consistent affects due to the high abundance of lost fishing gear (0.65 items m−2) directly entangled with structuring cnidarians. The artisanal and recreational fishing pressure are currently moderate. However, the use of bottom-contact fishing gear causes significant modifications to the seafloor’s integrity. This study emphasizes the high conservation value and vulnerability of the shoal, highlighting the importance of its protection through its inclusion in the Portofino MPA, whose external perimeter is 200 m from the study area. A critical discussion of the advantages and disadvantages is provided with a map of the possible extension of the MPA boundaries.