Submarine canyons are steep-sided “V’ or “U” shaped valleys that incise continental slopes worldwide. The geophysical and oceanographic features of submarine canyons can produce environmental conditions that cause benthic assemblages to be distinctive and productive compared to those of the adjacent slope; however the assemblages are potentially vulnerable to anthropogenic impacts, including bottom fishing. In order to help inform policy and management, submarine canyons need to be objectively defined topographically and their benthic assemblages characterised. A canyon network occurs off the Otago Peninsula, south-eastern New Zealand, but lack of detailed bathymetric data and adequate benthic sampling has limited study of the canyons. This thesis outlines a method of defining submarine canyon areas and examines epifaunal and infaunal assemblages of the Otago canyons and adjacent slope. Objective definition of the Otago canyon network in the GIS software GRASS along with the steps to use this methodology worldwide are described. Archival count data from 1966-74 on the epifauna are analysed using the PRIMER suite of programs to characterise epifaunal assemblages. Anomurans, polychaetes, asteroids and ascidians make up 70% of the epifaunal canyon assemblage. The epifaunal assemblage is clearly defined by water depth and recognisable from 380 m. Quantitative sampling of infauna in Saunders canyon, Papanui canyon and adjacent slope was carried out to examine infaunal community structure of the canyons and adjacent slope. Infaunal canyon assemblages are dominated by polychaetes, amphipods, ophiuroids, decapods and isopods in canyons, accounting for 75% of collected individuals. Polycheates, malacostraceans, ophiuroids and foraminifera comprise the bulk of collected infauna from the slope environment. A checklist of recorded species found in the Otago canyon network is appended.