Tuna fisheries were applied to an integrated ecosystem-based fishery risk assessment method using indexes of target species status, inhabited species in a target ecosystem, habitat quality and socio-economic benefit of affected fisheries. This study suggested more effective and efficient management measures to break away from traditional management methods, such as limitation of catch and fishing effort. The results presented that the objective risk index (ORIS) on sustainability of bigeye and yellowfin tunas by purse seine fishery was estimated high due to the high catch ratio of small fishes. The ORIs of biodiversity (ORIB) and habitat quality (ORIH) of purse seine fishery were also estimated at a high level from using fish-aggregating devices (FAD). However, due to skipjack tuna’s high catches, the ORI of socio-economic benefit (ORIE) was estimated at a very low level. Due to the high bycatch rate, ORIB was high, and ORIS and ORIH were evaluated at a low level in longline fishery. Due to strengthern of fishing restrictions and increase of fishing costs, the ORIE was assessed to be very high. The ecosystem risk index (ERI) for two tuna fisheries was assessed low, but the overall FAD management by purse seine fishery is necessary at the ecosystem level.