Deep reef assemblages in south-eastern Australia are poorly described, and have been surveyed by only a few studies conducted over small spatial scales. Here, we characterise the composition of deep (~30−90 m depth) sessile invertebrate communities from sub-tropical (27° S) to temperate eastern Australia (43° S). We estimated the cover of 51 preselected invertebrate types from over 1700 seafloor images collected by an autonomous underwater vehicle from >105 km of transects across the study region. Seafloor images were assessed using 3 alternative schemes reflecting different resolution of benthic invertebrate groupings, including the broadlevel Colla borative and Automated Tools for Analysis of Marine Imagery project (‘CATAMI’) classification recently developed as a generic scoring approach for seafloor imagery. Ordination using canonical analysis of principal coordinates indicated a clear latitudinal gradient in benthic community composition and, particularly when based on individual morphotypes, 3 distinct community types (sub-tropical, warm temperate and cool temperate). Changes in community structure mostly correlated with primary productivity and the temperature climatology, while local-scale variability in community composition was most related to depth. Along with the gradual shift in deep reef community composition across latitudes, region-specific sessile invertebrates might serve as useful indicators of change in these deep benthic communities under future changes in ocean climate in the region, which has been identified as a global hotspot for ocean warming. Our methodological approach has general applicability for large-scale surveying and monitoring of benthic communities using underwater imagery.