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.

Coastal fisheries in Korean waters have highly complexity with a variety of fishing gears, and scale of those fisheries is smaller than that of offshore fisheries. As a result, important spawning and nursery grounds for many species of fish has been destroyed. The pragmatic ecosystem-based approach was developed for the assessment of fisheries resources in Korean waters by Zhang et al. (2009; 2010). As for the species risk index (SRI), common squid caught by coastal gillnet in the Uljin region had the highest risk. As for the fisheries risk index (FRI), coastal gillnet in the Uljin coastal waters had the highest risk. For the common squid which had the highest SRI, resources management strategies must be established such as catch prohibition of length and period with TAC. For the coastal gillnet in the Uljin region which had the highest FRI, it is judged to need management plans for conserving biodiversity as reducing the catch of non-target species and discards. Also to protect existing habitat, illegal fishery should be prohibited, and fishing gears should be designed in the environmental-friendly way considering when fishing gears lost.

This study identified problems of the existing ecosystem-based fisheries assessment approach, and suggested new methods for scoring risk and for the estimation of fishery risk index. First, risk scores of zero to two for target and limit reference points for each indicator were replaced by those of zero to three, and the risk scores were calculated from new formulae which were developed in this study. Second, a new method for estimating fishery risk index (FRI) was developed in this study, considering the level of indicators. New method was applied to the Korean large purse seine fishery, large pair trawl fishery and drag net fishery. More precise and detailed risk scores were obtained from the new method, which can explain the risks by the wider range of both risk levels for 'better than target' and 'beyond limit'. The new method for estimating FRI could avoid the basic problem related with duplicated computations of fishery-level indicators, which improved the estimated FRI to be more accurate. Also, a method for estimating variance of FRI using the bootstrap was proposed in this study.

In the application of the ecosystem-based fisheries assessment Jeonnam marine ranching ecosystem, two fisheries, funnel fishery and trap fishery, were selected as target fisheries. Black seabream, Acanthopagru schlegelii, rock bream, Sebastes inermis, gray mullet, Mugil cephalus, were selected as target species for the funnel fishery, and conger eel, Conger myriaster, was target species for the trap fishery. For assessing indicators of four management objectives, that is the maintenance of sustainability, biodiversity, habitat quality and socio-economic benefits, indicators were selected considering the availability of data, which were 5 indicators for sustainability, 3 indicators for biodiversity, 4 indicators for habitat, 2 indicators for socio-economic benefit. The Objective risk indices for sustainability and biodiversity of two fisheries were estimated at yellow zone, medium risk level. The objective risk indices for habitat and socio-economic benefit were estimated at green zone, safe level. The species risk indices (SRI) were estimated at yellow zone. The fishery risk indices (FRIs) were estimated at 1.143 and 1.400 for funnel net fishery and trap fishery, respectively. Finally the ecosystem risk index estimated at 1.184.