Biodiversity and the ecological and evolutionary processes which influence faunal distributions are poorly understood in deep-sea habitats. This thesis assesses diversity of deep-sea amphipod crustaceans at three taxonomic levels (family, species, genetic) on continental margins of New Zealand relative to environmental variables. Sampling was undertaken at 20 stations located on Chatham Rise and Challenger Plateau, two major geomorphic features with contrasting environmental conditions. In Chapter 1, total diversity of the >12,500 amphipods assessed at the family-level revealed high abundance (range: 44 – 2074 individuals 1000 m⁻²) and taxonomic richness (27 families). Amphipod assemblages at all stations were largely dominated by the same families. Chatham Rise stations were mostly similar in family composition to one another and to the two closest Challenger Plateau stations. Overall, amphipod community composition correlated most strongly with surface chlorophyll a, suggesting strong benthic-pelagic coupling. In Chapter 2, I used molecular methods (COI DNA sequence thresholds of 6%) to estimate species diversity in the dominant amphipod family identified from Chapter 1 - the Phoxocephalidae. Analyses revealed 49 putative species-level taxa, which greatly exceeds the current number (n=17) of formally described New Zealand phoxocephalid species. A cluster of stations with highly similar taxa was identified, broadly distributed over the crest of the Chatham Rise, in association with elevated food availability. Similar to the family-level analyses of Chapter 1 multivariate analysis of phoxocephalid assemblages and environmental parameters revealed a strong correlation with measures of food supply. Analyses of inter-station assemblages revealed a major split between regions, indicating minimal overlap in taxon distributions on eastern and western continental margins. Chapter 3 examined genetic connectivity among deep-sea habitats. A phylogenetic analyses of three relatively abundant and widespread taxa; cf. Ampelisca chiltoni, cf. Oediceroides apicalis and Phoxocephalidae sp., was combined with available genetic data from a further 61 taxa collected from the same stations, to examine mean levels of inter-station genetic divergences. Nearly identical levels of genetic divergence were found between eastern and western regions for all three taxa. Furthermore, inter-station analysis of the wider amphipod community revealed similar patterns of genetic structure in most taxa. Based on molecular clock estimates, genetic divergences most likely corresponded to isolation following landmass changes during the Pleistocene. This thesis research has revealed a biodiversity hotspot on New Zealand continental margins. I conclude that Cook Strait and the subtropical front are important structures responsible for shaping benthic communities on New Zealand continental margins and that vicariance is likely to have played an important role in the evolutionary radiation of the New Zealand deep-sea fauna.