Discoveries of the larvae of the European and American eels, Anguilla anguilla and A. rostrata, in the Sargasso Sea and of the Japanese eel, A. japonica, in the Philippine Sea indicate that these freshwater eels migrate thousands of kilometres into the open ocean to spawn. Here we pinpoint a spawning location for Japanese eels after genetically identifying newly hatched larvae that we collected from the site. The restricted size of this spawning area ensures that the eel larvae enter a particular current that transports them to the freshwater areas in east Asia where they mature, and it also prevents them from being carried southwards away from their species range by a different local current.