The composition and structure of megabenthic communities in the Blanes canyon and adjacent open margin (Northwestern Mediterranean) were studied. The aim was to assess the effect of the canyon and commercial fishing intensity on the community composition and structure of benthic megafauna by (i) describing the megabenthic community composition, (ii) quantifying faunal abundance and biomass and (iii) describing community structure with MDS analyses and biodiversity indices. The results are compared between three sites (canyon head, canyon wall and open margin) located between 435 m and 700 m. Samples were collected using a commercial bottom trawl between April 2003 and March 2004. These sites are exploited by the local fishing fleet that targets the rose shrimp Aristeus antennatus. A total of 131 megabenthic species were identified from the three sites, with fishes and decapod crustaceans being the most speciose, most abundant and of higher biomass. The species richness, abundance and biomass of non-crustacean invertebrates were low. There were no significant differences in total abundance and biomass between the three sites. However, community structure analysis suggests that the open margin community is significantly different from the canyon head and canyon wall, with a lower species richness, lower diversity and lower evenness. The open margin community also reflects a higher degree of disturbance compared to the two canyon habitats. The results indicate that there is a canyon effect on the community structure of benthic megafauna, but this may be modulated by differing fishing pressure, which adds an additional factor to margin heterogeneity.