Deep-water corals are known to provide essential habitat for fish and invertebrates along the continental slope in different areas of the world, offering prey to coral predators, protection or attachment substrate to other suspension feeders. In the Mediterranean Sea the coral Isidella elongata (Esper, 1788) characterizes a facies of bathyal compact mud substrates between 500 and 1200 m depth. Based on 4 experimental surveys carried out between 1985 and 2008, we obtained quantitative data on the fauna associated with live coral stands. We show that species richness of invertebrates and crustaceans, as well as abundance and biomass of crustaceans, is higher in areas with large stands of the coral. Some commercial fishery species are also more abundant or reach larger sizes in areas with high density of the coral, particularly the red shrimps Aristeus antennatus (Risso, 1816) and Plesionika martia (A. Milne Edwards, 1883). Trawling over I. elongata facies causes direct impacts on the biological assemblages by removing the habitat-forming corals, decreasing invertebrate species diversity and negatively affecting fisheries production in the long term.