The movements, and hence stock structures, of bigeye tuna, Thunnus obesus, and yellowfin tuna, Thunnus albacares, remain poorly defined despite their importance to food security, livelihoods and government revenue in many nations. We examined the parasite fauna of juvenile bigeye tuna and juvenile yellowfin tuna from areas within and outside Indonesia to determine how far they may have moved since metamorphosis and acquisition of a piscivorous diet. Patterns in parasite data between collection areas were consistent between the two tuna species. Fish from two outlier areas, Maldives and the Solomon Islands, harboured a distinct parasite fauna from those from adjacent Indonesian areas, although occasionally showed similarity with those from within the Indonesian archipelago. Within Indonesia, the parasite data indicated that few juvenile fish moved west from the Pacific Ocean into the archipelago and few moved west from the archipelago into the eastern Indian Ocean. While sampling of adult fish is required to fully resolve the stock structure of both tuna species, the results provide a necessary first-step in examining structuring of the two tuna species in Indonesia and indicate that juveniles of both species may have more restricted movement than is recognized in current management arrangements.