High-latitude coral reefs (HLCRs) are unique ecosystems with diverse biological assemblages, including many low latitude species on their distribution margins. These ecosystems are threatened by fisheries exploitation, habitat destruction and climate change; however, relative to low latitude coral ecosystems, our understanding of their structure and functioning is limited. This is particularly true for sharks and rays. In this study, we used baited remote underwater stereo-video systems to determine the effect of habitat and management on the assemblage structure of elasmobranchs on the HLCRs of southern Africa (26-28°S; iSimangaliso Marine Protected Area [MPA], South Africa, and the adjoining Ponta do Ouro Partial Marine Reserve, Mozambique). We recorded a total of 12 species of shark (142 individuals) and 9 species of ray (40 individuals) over 2 brief time frames (November 2016 and June 2017). All species were tropical with many on the southern limit of their known distributions. Sharks increased in diversity with depth and showed a preference for the reef and mosaic habitats, relative to sand. The occurrence of rays was predominantly influenced by the presence of low relief habitats. These findings highlight the need for MPAs to encompass both sand and reef habitats over broad depth ranges to effectively protect elasmobranch assemblages. We found evidence to support the high average abundance and diversity of sharks and rays within MPAs of South Africa and southern Mozambique. The results highlight the importance of marginal HLCRs, particularly those within MPAs, for the management and conservation of tropical elasmobranch species.