1. The structure of food webs provides important insight into biodiversity, organic matter (OM) pathways, and ecosystem functioning.
2. Stable isotope analysis (δ13C and δ15N) was used to characterize the trophic structure and the main OM pathways supporting food webs in the Rapa Nui coastal marine ecosystem.
3. The trophic position of consumers and isotopic niche metrics were estimated for different assemblages (i.e. mesozooplankton, emergent zooplankton, reef invertebrates, reef fishes, pelagic fishes, and seabirds). Furthermore, the relative importance of different OM sources (i.e. macroalgae, zooxanthellate corals, and particulate OM [POM]) was assessed for heterotrophic consumers using Bayesian mixing model (MixSIAR).
4. Results show a clear pattern of 13C and 15N enrichment from small‐sized pelagic and benthic invertebrates, to reef and pelagic fishes, and seabirds. Most invertebrates were classified as primary consumers, reef fishes as secondary consumers and pelagic predators and seabirds as tertiary and quaternary consumers.
5. Isotopic niche metrics indicate a low trophic diversity for pelagic assemblages (mesozooplankton and pelagic fishes), in contrast to reef fauna (invertebrates and fishes), whose higher trophic diversity suggest the exploitation of a wider range of trophic resources. Overlapping of standard ellipses areas between reef invertebrates and reef fishes indicates that both assemblages could be sharing trophic resources.
6. Mixing models results indicate that POM is the main trophic pathway for mesozooplankton, macroalgae (Rhodophyta) for emergent zooplankton, and a mix of coral‐derived OM and Rhodophyta for coral reef assemblages such as macrobenthos and reef invertebrates. In contrast, POM contribution was notably more important for some pelagic fishes and seabirds from upper trophic levels.
7. This study provides key elements for conservation efforts on coral reefs, management planning and full‐implementation of the recently created Rapa Nui Multiple Use Marine Protected Area.