In the Bay of Biscay, Cold Water Coral (CWC) habitats have been mapped in 24 out of a hundred known submarine canyons. The footprint of ROV or towed-camera transects is small compared to the size of these canyons but still, known CWC habitats totalize a linear of 46 km. The distribution of these habitats, dominated by reef-building scleractinians, antipatharians, alcyonaceans and pennatulids, is however patchy and their median size is small, ranging from 6 to 65 m. While the preservation of these Vulnerable Marine Ecosystems has become essential, all CWC habitats will not be benefit from conservation strategies due to their widespread and patchy distribution. Priorities must thus be defined. Among the criteria for such prioritization, we explore here the ecological role of CWCs as ecosystem engineers.The abundance, the diversity and the taxonomic composition of megafaunal assemblages associated with each CWC habitat are compared. Scleractinian reefs, antipatharians and alcyonaceans on hard substrates as well as pennatulids on soft substrates host different megafaunal assemblages and each should be considered as separate management units. Within each of these three units, we further test the influence of coral cover or coral density, as well as the influence of patch size, on the abundance and the diversity of the associated fauna. In the different habitats, the megafauna shows different patterns according to coral cover, coral density and habitat size, suggesting that aggregations of CWCs do not all have the same ecological role within submarine canyons. The consequences for conservation prioritization are discussed.