Oceanic islands sustain biodiversity of global conservation value, such as unique assemblages and endemic species at high risk of extinction, including along their intertidal rocky reefs. In these isolated and often under-resourced locations, there is generally little information to support the management of biodiversity on these reefs. The World Heritage listed Lord Howe Island Marine Park presents a unique opportunity to better understand the patterns, value and vulnerability of oceanic island biodiversity. Reefs representing habitat types common to oceanic islands were aerially mapped. These included boulder, rubble and platform reefs of basalt and calcium carbonate within lagoonal, open coastline and offshore wave environments. Timed searches of solitary macro-invertebrates were then undertaken within geo-located plots over 15,600 square metres. High levels of diversity (215 species) and endemicity (9% of species) were recorded, and most endemic species had small or habitat restricted populations. Strong differences in biodiversity occurred across habitat types, with those formed from coral rubble supporting greatest species richness, taxonomic diversity, and number of rare and vulnerable species. These findings have implications for marine protected area planning on oceanic islands, such as using fit-for-purpose methods to record biodiversity, representing distinct reef types including rubble habitats, and protecting vulnerable endemic taxa.