Aquaculture of Japanese eel Anguilla japonica relies upon the natural recruitment of their glass eels (juveniles); however, predation that could influence glass eel recruitment remains unknown. In the present study, we aimed to elucidate the proportion of predation on A. japonica glass eels through stomach content analysis of predatory fishes collected in the estuary region of the Tone River system and its vicinity in Japan. Species of the predated glass eels were identified by DNA barcoding. A total of 270 predatory fishes of 15 taxa was collected over 2 years. The overall proportion of predation on glass eels, genetically identified as Japanese eel, was 0.7%, but this rose to 2.0% when data were limited to fishes caught during the peak months of glass eel recruitment. A glass eel was found in the stomach contents of a channel catfish Ictalurus punctatus, an invasive species in this river system, and a blackfin sea bass Lateolabrax latus. These fishes are therefore considered potential predators of A. japonica glass eels. However, as the proportion of predation was low, and the glass eels represented only small proportions of predator stomach contents, further investigation is needed for a better understanding of predation on A. japonica glass eels, and its effects on the early life stages of this endangered species.