To investigate relationships between epibenthic macrofauna and bathyal habitat characteristics, we examined the abundance, diversity and community composition of amphipod crustaceans relative to environmental variables on two major bathymetric features of New Zealand – the Chatham Rise and Challenger Plateau. An epibenthic (Brenke) sledge was used to sample depths ranging from 200 to 1200 m. Fifteen stations were sampled on the Chatham Rise, which is an extensive submarine ridge, east of New Zealand, characterised by high productivity in surface waters, associated with the Subtropical Front. Five stations were sampled on the Challenger Plateau, west of New Zealand, a region with a similar depth range, but less topographical relief and lower pelagic productivity relative to the Chatham Rise. Over 12,500 amphipods were recovered and identified. We found high abundance (range: 44–2074 individuals 1000 m−2) and taxonomic richness (27 families) in both regions. Amphipod assemblages at all stations were largely dominated by the same families, particularly the Phoxocephalidae. Chatham Rise stations were mostly similar in family composition to one another and to the two closest Challenger Plateau stations. However, the remaining three, more distal, western Challenger Plateau stations were highly differentiated from other stations and from one another, despite being relatively similar habitats. Overall, amphipod community composition correlated most strongly with surface chlorophyll a, suggesting strong benthic–pelagic coupling and emphasising the importance of benthic–pelagic links in bathyal ecosystems.