Some anguillid eels migrate thousands of kilometers from their spawning grounds, dispersing across vast geographic areas to fresh and brackish water habitats, where they settle and grow. Japanese eels (Anguilla japonica) and giant mottled eels (A. marmorata) are both found in Japan, although their distributions differ, and their exact distributions are poorly known. We assumed that topographic distribution patterns of Japanese and giant mottled eels must differ among and within rivers along the northwest coast of Kyushu, Japan. Environmental DNA (eDNA) analysis was conducted at 87 sites in 23 rivers. Japanese eel eDNA was detected in 19 rivers (82.6%) and that of giant mottled eels was detected in eight (34.8%). We detected giant mottled eel eDNA in five rivers where they were previously unknown. eDNA for Japanese eels was detected at six of nine sites in the north (66.7%), 13 of 23 sites in Omura (56.5%), and 37 of 55 sites in the south (67.3%). In contrast, giant mottled eel eDNA was detected at one of nine sites in the north (11.1%), no sites in Omura, and 15 of 55 sites in the south (27.3%). There was no correlation between eDNA concentrations of the two species at 10 sites in the five rivers where eDNA of both species was detected. These findings suggest differences in the distribution of the two eel species and the northern distributional limit of giant mottled eels in the area facing the East China Sea.