International efforts are currently being made to establish networks of marine protected areas (MPAs) for the purposes of conservation of marine biodiversity. One of the primary objectives of MPA networks is to achieve representation of all marine biological diversity. Since we do not know the extent of biological diversity nor its distribution and function, we use surrogates to represent biological diversity. At a broad scale, measures of the physical environment are used, however at a fine scale biological assemblages have been shown to provide better representation of known biological diversity. While there are well known descriptions of assemblages for shallow water environments, few such descriptions of deep-sea benthic assemblages have been attempted. This paper provides descriptions of deep-sea epibenthic megafaunal assemblages based on a broad-scale video and stills image survey of the upper bathyal (200–1000 m) regions of the Rockall Trough and eastern Faroe–Shetland Channel. One thousand nine hundred and eighty-seven images were analysed from 139 video transects sampled from Dangaard and Explorer Canyons, Rosemary Bank Seamount, Hatton Bank, Wyville-Thomson Ridge, and the continental slope west and north-west of Shetland. Quantitative data obtained were analysed using cluster analysis and SIMPER analysis in Primer V.6 to identify benthic assemblages and their characterizing species. Thirty-one epibenthic megafaunal assemblages are defined by their characterizing species, and their distribution in terms of site, depth, temperature and substratum type. These 31 ‘biotopes’ provide consistent units for use in biological mapping efforts and assessments of representativeness in MPA network design. To facilitate the incorporation of these biotopes into existing deep-sea classification systems the biotopes have been assigned to broad substratum types. This is consistent with the use of substratum as a surrogate in many existing systems.