Little is known about diversity patterns of biological assemblages in deep-sea environments, primarily because sampling deep-sea biota over vast areas is time consuming, difficult, and costly. In contrast, physical mapping capabilities are increasing rapidly, and are becoming more cost-effective. Consequently, the growing need to manage and conserve marine resources, particularly deep-sea areas that are sensitive to anthropogenic disturbance and change, is leading the promotion of physical data as surrogates to predict biological assemblages. However, few studies have directly examined the predictive ability of these surrogates. The physical environment and biological assemblages were surveyed for two adjacent areas – the western flank of Lord Howe Rise (LHR) and the Gifford Guyot - spanning combined water depths of 250-2200 m depth on the northern part of the LHR, in the Coral Sea. Multibeam acoustic surveys were used to generate large-scale geomorphic classification maps that were superimposed over the study area. Forty towed-video stations were deployed across the area capturing 32 h of seabed video, 6229 still photographs, that generated 3413 seabed characterisations of physical and biological variables. In addition, sediment and biological samples were collected from 36 stations across the area. The northern Lord Howe Rise was characterised by diverse but sparsely distributed faunas for both the vast soft-sediment environments as well as the discrete rock outcrops. Substratum type and depth were the main variables correlated with benthic assemblage composition. Soft-sediments were characterised by low to moderate levels of bioturbation, while rocky outcrops supported diverse but sparse assemblages of suspension feeding invertebrates, such as cold-water corals and sponges which in turn supported epifauna, dominated by ophiuroids and crinoids. While deep environments of the LHR flank and lower slopes of the Gifford Guyot were characterised by bioturbation with high occurrences of trails, burrows, and mounds, evidence for bioturbation was significantly less on the upper sections of Gifford Guyot, with mostly trails on the more sediment starved environments. The seamount summit also supported a variety of taxa, such as benthic ctenophores and rock-associated fishes that were not recorded in the deeper basin habitats. Physical characteristics of the seabed, particularly geomorphology, were good predictors of biological assemblage composition and percent cover of key taxa. Of the nine geomorphic classes assessed in this study, six predicted different physical habitats that supported distinct biological assemblages. However, other classes that were defined by spatial features (e.g., valleys, seamount dunes) where surficial physical variables were not unique, provided little predictive power of biological assemblages, but rather had characteristics that were shared with adjacent/surrounding geomorphic classes. Given the growing need to use surrogates in the management and conservation of marine environments, these results are promising. However, our findings suggest that there is a pressing need for careful testing and validation of surrogates, such as geomorphic classes, before classification schemes can be deemed effective and employed as a management tool to predict seabed habitats and their biological assemblages.