The distribution and abundance of benthic megafauna in areas known to be inhabited by dense gorgonian coral assemblages were examined at Northeast Channel, off Nova Scotia, Canada, in August 2001. Using a remotely operated vehicle, 1–5 video transects during each of 1–2 dives at each of four sites (Rips, Middle Canyon, Hell Hole West and Hell Hole East) were conducted. The relationships in the structure of biological assemblages at three spatial scales: within transects (10s of metres); between dive locations (100s of metres); and among sites (10s to 100s of kilometres) were explored. The most abundant epibenthic taxa included the gorgonians Primnoa resedaeformis and Paragorgia arborea, several suspension feeders (Actinauge verrilli, Bolocera tudiae, an unidentified anemone and encrusting sponge, Ophiacantha abyssicola), the deposit feeder Porania pulvillus insignus and the predatory Solaster endeca. The basket star Gorgonocephalus arcticus was present only on colonies of Paragorgia arborea. Despite large variability in abundance and assemblage composition among transects and dive locations, clear patterns were observed among sites. Mean abundance of most cnidarians and echinoderms was greatest at Hell Hole West. No gorgonians were found at Hell Hole East. The encrusting sponge was most abundant at the Rips and least abundant at Hell Hole East. Cluster analysis and multidimensional scaling (MDS) indicated that, when abundance was averaged across transects for each dive, the megafaunal assemblages fall into groups of dives that separated by site. These differences among sites are most likely related to variability in the physical environment. The epibenthic megafaunal assemblages were as diverse in the presence as in the absence of gorgonian corals, at least at the abundances that we observed. However, the apparent low recruitment and abundance, combined with small population size make these assemblages particularly vulnerable to perturbations.