In 2014, the continental shelf and submarine canyon off Cap de Creus (NW Mediterranean) were included in the Site of Community Importance (SCI) “South-West Gulf of Lions canyons system” of the Natura 2000 Network of protected areas. Before the declaration of the SCI (2007-2103), 60 underwater video transects were performed in the area by means of ROVs and a manned submersible, covering more than 30 km of seafloor. Based on the annotation of the video images, we identified the main invertebrate megabenthic communities dwelling from the shelf (70 m depth) down to the bottom of the canyon head (400 m depth). The results of the multivariate analyses indicated that this marine area hosted several benthic communities dominated by suspension- and filter-feeding species, including octocoral gardens, soft-coral assemblages, crinoid fields, sponge grounds and cold-water corals. This dataset includes (1) the geographical location of the benthic communities identified in the video footage, as determined by the clustering analysis, (2) the intra-community diversity associated to the benthic communities, provided as the number of megafauna species identified in each sampling unit and the exponential of Shannon, and (3) the spatial distribution of the benthic communities mapped by means of the Random Forest classification algorithm. This dataset is related to the article “Diversity, structure and spatial distribution of megabenthic communities in Cap de Creus continental shelf and submarine canyon (NW Mediterranean)” submitted to Progress in Oceanography by Dominguez-Carrió et al., which contains further information on how the data were obtained and processed.