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The Juan Fernández Archipelago (33°37'S, 78°51'W), an isolated group of islands 650 km west of continental Chile, has a high degree of endemism in its marine biota. Despite numerous scientific expeditions to these islands that have identified this high endemism, few studies have attempted to identify patterns of community structure in subtidal habitats. Using visual census, we surveyed fish and habitat associations at five sites located at two of the three islands of the archipelago. Given the isolation of the archipelago we asked: What is the composition of the reef fish fauna at these isolated islands? What habitats dominate subtidal environments? What influences the abundances of reef fishes? Our analysis confirms that fish communities at the archipielago are dominated by endemic species. The ichthyofauna is comprised of a mixture of subtropical and temperate taxa, with greater similarity to western than eastern South Pacific fauna. We identified different fish assemblages at wave-exposed and wave-sheltered sites. Brown and red macroalgae were correlated with the abundances of some reef fishes. Four broad trophic categories of reef fishes were present at the archipelago, with invertebrate consumers dominating abundance. To our knowledge, this is the first attempt to quantify patterns of community structure in subtidal environments at the Juan Fernández Archipelago.