Fish eggs have a wide range of predators. However, observing these predators is challenging, as is identifying fish eggs based on morphological traits. In this study, we observed hydroids, which are sessile organisms, consuming pelagic fish eggs. We conducted cytochrome c oxidase I (COI) metabarcoding to identify both the predator and the prey species. Massive COI reads were de novo assembled and nine representative sequences were constructed. The predator, identified from the representative sequences and its morphological features, was determined as Ectopleura crocea. The fish eggs that had been preyed upon belonged to two species: Sillago japonica and Parajulis poecilepterus. Additionally, four arthropod species (Labidocera rotunda, Oithona similis, Paracalanus parvus, and Pseudevadne tergestina) were consumed, and their morphological traits could not be observed, due to digestion. COI metabarcoding was an effective tool for studying the feeding activity of these small predators.