Temperate mesophotic ecosystems (TMEs) that occur in the deeper (>30 m) waters of shelf seas are challenging ecosystems to study due to accessibility and the increased cost compared to shallower water marine ecosystems. These limitations are exacerbated in high energy coastlines, such as the Great Australian Bight (GAB), where large swells can limit boat access and make deployment of sampling devices risky. Our research focuses on Autonomous Underwater Vehicle (AUV) footage that assessed benthic communities residing in the mesophotic zone of southern Australian shelf seas, with a particular focus on the GAB and locations around Tasmania. We describe megaripple-like benthic structures as habitat for sessile epifauna and compare the community composition of these megaripple-like structures to the communities occurring on other local benthic habitats (e.g. rocky outcrops, sponge grounds). Overall, we found complex epifauna communities on these structures (e.g. megaripple peaks, sponge grounds and rocky outcrops) versus bare sand and troughs. The results of this study are instrumental in further understanding of benthic features in the mesophotic zone of temperate shelf seas. It highlights the importance of multiple habitats as complex benthic communities throughout the mesophotic zone, which should be considered in ecological assessments and management plans into the future.