Japanese eel, Anguilla japonica - an endangered species, is a catadromous fish spawning at the oligotrophic "desert of the ocean" in the northwestern Pacific. For clarifying natural diets, the composition of larval eel gut contents was compared with seawater in the locality by the next-generation 18S rRNA gene sequences. Both primary components were dinoflagellate, the gut contents showed a relatively high abundance of zooplankton, which suggested the particulate organic matter to be a food source. Composition of gut contents showed no geographical difference and most similar to seawater of chlorophyll maximum depth. By extensively oceanographic observation in eel larvae feeding area, chlorophyll maximum was formed the upper part of the thermocline, where showed optimum temperature for the leptocephalus development. Chlorophyll maximum layer is estimated to be the feeding environment of eel larvae from both food and growth. Thus, much migratory fish may prefer the tropical oligotrophic ocean as spawning and nursery grounds.