The coralligenous reef represents one of the most important coastal marine habitats in the Mediterranean in terms of associated biodiversity and the ecosystem services it provides, being capable of creating an extremely complex and diverse seascape. However, it is highly vulnerable to mechanical damage, particularly from fishing activities. Within a collaboration agreement between the Capo Carbonara Marine Protected Area (MPA) and the University of Genoa, a protocol was developed to assess the biophysical damage (disvalue) caused by Abandoned, Lost or otherwise Discarded Fishing Gear (ALDFG). Starting from the natural capital values of the MPA habitats, estimated through the application of the environmental accounting protocol developed by Vassallo et al. (2017), the ecological loss of natural capital caused by ecosystem degradation due to ALDFG was assessed. For this purpose, the natural capital of coralligenous reef was assessed modeling the food web and accounting for the resources required over space and time for its generation. To quantify disvalue, four samples of ALDFG, removed from the coralligenous reef by MPA staff, were analyzed using the same methodology. Specifically, the biomass of the benthic communities associated with the ALDFG was quantified and the impacted surfaces were estimated as input data for the calculations. The results showed an average disvalue associated with ALDFG of 1.12E+12 sej/m². The analyses revealed considerable variability among the different samples, bryozoans accounted for the largest proportion of the biomass analyzed, consequently, the largest contribution was associated with the heterotrophic component. Finally, a comparison was made between ALDFG disvalue and the values of total coralligenous natural capital in the MPA (6.14E+12 sej/m²): this comparison revealed an 18% loss of natural capital. This confirms the importance of targeted monitoring activities of anthropogenic impacts on this habitat, particularly those related to fishing activities.