Cumulative impacts on southern ocean (SO) seafloor habitats demand the identification, quantification, and tracking of areas that are representative of surrounding biodiversity and ecosystem functions. Regions of the SO benthos that contain aggregations of sessile organisms with complex three-dimensional (3D) morphologies or structures are known to act as habitats for multiple fauna from different trophic levels. Because of the logistical and environmental challenges associated with SO benthic surveys, researchers are increasingly relying on underwater vehicles and imaging systems to collect information. However, quantifying the degree of habitat provided by the unique SO benthic fauna remains a challenging task. In this study, we quantified the structural complexity of a SO polychaete reef (3 to 40 m depth). Overlapping images from the benthos were collected using a remotely operated vehicle and action cameras to build 3D models of the seafloor via "Structure-from-Motion" photogrammetry. This study is the first to quantify the structural complexity of a SO reef using photogrammetry and geographical analysis. We show the potential of this technique to identify areas with high structural complexity and possible biodiversity hotspots on the SO seafloor.