The National Biodiversity Strategy developed in Chile aims to protect 10% of the surface area of the most relevant marine ecosystems. The waters around the Juan Fernández Archipelago were not protected until 2014, when a Multiple Use Marine Protected Area was created in the 12 nautical miles around the archipelago, which includes five marine parks in sites of high conservation value. Three of these parks are located around Robinson Crusoe Island. This study aims to define a baseline for monitoring the impact of the marine protected area and provides ecological information to improve the understanding of coastal marine ecosystems around Robinson Crusoe Island. In addition to a characterization of bathymetry and habitats, intertidal and subtidal communities were sampled using transects and quadrats within the marine parks. We quantified species richness and abundances, which were later organized into functional groups for algae and trophic groups for mobile organisms. Although species richness did not vary between sites nor among the habitats sampled, we observed important differences in species abundance and composition as well as in functional and trophic groups both between sites and habitats. Among our results, we highlight: a) the dominance of endemic algae in intertidal and subtidal (mainly corticated and corticated foliose) habitats, b) high abundances of macroinvertebrate herbivores in intertidal habitats and detrivores in subtidal habitats, c) dominance of invertivorous fish in the subtidal, which are the primary predators of mobile benthic organisms. This characterization includes both the inter and subtidal coastal communities of the Juan Fernández Archipelago.