Context. Increasing interest in mesophotic coral ecosystems has shown that reefs in deep water show considerable geomorphic and ecological variability among geographic regions. Aims. We provide the first investigation of mesophotic reefs at the southern extremity of the Great Barrier Reef (GBR) to understand the biotic gradients and habitat niches in the lower mesophotic zone. Methods. Multibeam data were used to target five benthic imagery transects collected in the lower mesophotic (80–130 m) zone from the shelf edge near One Tree Island (23°S, 152°E) by using a single HD-SDI subsea camera. Key results. Transects supported similar benthic communities in depths of 80–110 m, with the abundance of sessile benthos declining below ~110 m where the shelf break grades into the upper continental slope. Conclusions. The effect of the Capricorn Eddy may be promoting homogeneity of benthic assemblages, because it provides similar environmental conditions and potential for connectivity. Variation in benthic communities between hard and soft substrate and differing topographic relief within the study site are likely to be influenced by variation in sedimentation, including sensitivity to suspended particles. Implications. This study highlighted that the lower mesophotic region on the One Tree shelf edge supports mesophotic coral ecosystems that vary depending on depth and substrate.