In the Mediterranean Sea, the coralligenous is an extremely important habitat for its biodiversity and role in carbon sequestration. However, coralligenous biocenosis is sensitive to many anthropogenic impacts, among which one of the major threats is the marine litter. The aim of the present work was to evaluate the marine litter present in the coralligenous habitat of the Marine Protected Area (MPA) Isole Ciclopi (Sicily, Italy). Through the analysis of frames obtained by Remotely Operated Vehicles (ROV) videos, data on the type of marine litter, grade of organisms’ coverage, litter-organism interactions, and seabed coverage of items were gained. Through ROV surveys, a low number of marine litter items was observed and most of them were fishing gears. On the found items there was a high degree of organisms’ coverage, which suggests that probably the marine litter was abandoned or lost since a long time. Overall, it was observed that in recent years the fishing activity in the MPA has not affected the coralligenous habitat. The present study represents a baseline for future monitoring programmes, which will be useful to develop protection measures and sustainable fishing, in order to preserve the coralligenous habitat of the MPA.