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Abstract Submarine canyons are important sources of habitat heterogeneity on the slopes of continents and islands, but the study of canyon ecology has been largely restricted to continental margins. Here we use visual and video surveys from 36 submersible dives to evaluate the role of canyons as abundance and diversity hotspots for megafauna in the Hawaiian Archipelago, an island chain embedded in an oligotrophic ocean. We surveyed megafauna in canyon and slope settings at depths of 350–1500 m along the margins of four islands: the low ‘islands’ of Nihoa and Maro Reef, and the high islands of Oahu and Moloka’i. Megafaunal communities in canyons differed significantly from those in nearby slope habitats at all depths. Highly mobile fishes and invertebrates were consistently more abundant in canyons than on nearby slopes at the same depth off all islands, suggesting that canyons may be important sources of larvae for surrounding habitats. In the few cases where megafaunal abundances were similar or higher on the slope, the differences were typically driven by higher slope abundance of sessile suspension feeders or animals with limited mobility, i.e. by organisms which are likely to have difficulty with high currents and sediment transport in canyons. Megafaunal species richness and diversity generally trended higher within canyons, especially for the highly mobile taxa. Canyons contained 41 megafaunal species never observed on the slope, and increased estimated regional species richness by 25–30 species, indicating that canyons enhanced beta and gamma (regional) biodiversity. An expected trend of greater enhancement of diversity and abundance in canyons on the margins of high versus low oceanic islands was not observed, although megafauna were generally more abundant in both canyon and slope habitats on the high islands (Oahu and Moloka’i). We conclude that submarine canyons on both low and high islands in the Hawaiian Archipelago may provide keystone structures, enhancing megafaunal abundance, providing source populations for the open slope, and enhancing local and regional species diversity.