The aim of this study was to examine the possible interspecific interactions between the freshwater eel Anguilla japonica and the marine conger eel Conger myriaster. Spatial distribution, foraging time, and diet were compared between 380 A. japonica and 221 C. myriaster juveniles in a large brackish water bay and a tributary river estuary. Almost no C. myriaster were caught in the estuary, but both species coexisted in the bay at similar densities. For both species, percentages of eels with stomach contents were greater in the morning than in the afternoon, indicating they forage at night. Both species mainly fed on benthic crustaceans in the bay, but the size of the main prey species, mud shrimp Upogebia major, was significantly larger in A. japonica. The difference in prey size appears to be related to the eel body size (A. japonica: 559.5 ± 88.0 mm, C. myriaster: 356.4 ± 56.0 mm), which probably reflects the differences in the life history-related movements of these eels, with A. japonica using the bay at large sizes and C. myriaster using the bay as a nursery area before moving to deeper water. The differences in their migratory and movement patterns may result in niche segregation in the brackish bay where both species coexist.