These samples contain environmental DNA (eDNA) sequences from seawater and surface sediment collected across coral reef ecosystems in Indonesia (Lombok, Wakatobi, Misool, and Waigeo regions). Samples were amplified with the Leray COI primers (Leray et al. 2013, Front. in Zool.) to characterize enumerate metazoan biodiversity. Data were used to get preliminary information on coral reef metazoan biodiversity as well as evaluate the current utility of marine eDNA research in Indonesia.