Multibeam sonar has great potential for remote characterisation of seafloor habitats and fauna but interpretation is highly scale dependent. Under the Ocean Survey 20/20 programme (OS 20/20) New Zealand is collecting multibeam data combined with physical seabed samples across large areas of its Exclusive Economic Zone (EEZ). We used multibeam echosounder (MBES) transects from the Chatham Rise and Challenger Plateau together with nested biological sample data to explore the potential of vessel-mounted MBES for remote characterisation of seabed biological assemblages and habitats in the deep-sea. The MBES transects extend over 1000s km laterally and from ca. 250 to 1800 m depth. At 150 sites nested within these transects, seabed biological assemblages and substrates were sampled, primarily by video transect and epibenthic sled.