We compared multi-assay metabarcoding sequences of environmental DNA (eDNA) isolated from seawater and partially digested gut items from an obligate corallivore butterflyfish (Chaetodon lunulatus) resident at coral reef sites in the South China Sea. We specifically tested the proportional and statistical overlap of the different approaches (seawater versus gut content metabarcoding) in characterizing eukaryotic community composition on coral reefs based on 18S rRNA and ITS2 rRNA sequence data.