Behavioural experiments using artificial and natural stream channels were undertaken to determine whether there were differences in dispersal between newly emerged male and female masu salmon. Eyed eggs from a cross with wild spawners were planted in the middle pool of an artificial channel. After emergence, more males than females moved into an upstream trap, while fewer males moved downstream. In a natural stream, eyed eggs were marked with alizarin complexone to distinguish them from naturally spawned eggs and these were planted into artificial redds. More newly emerged male fry remained at the planted site than female fry. In contrast, more females moved downstream than males. These results imply that differences in dispersal patterns between male and female masu salmon fry are genetically controlled.