Considering the negative impact of IUU fishing on fishery resources and fishery management, a revised approach for estimating risks of the ecosystem-based fisheries assessment (EBFA) of Zhang et al. (2011) was developed that incorporates three components of the IUU (illegal, unreported and unregulated) fishing as penalties. In this study, we introduced ways to develop indicators of IUU fishing suitable for the Korean fishery and apply them to ecosystem-based resource assessment. The indicator for the illegal fishing component was set as the fishing without licenses or permits, and that for the unreported fishing component was set as unreported fishing activities. Indicators for the unregulated fishing component were set as fishing operated by illegal fishing gear, illegal fish capture, fishing operations in prohibited fishing area, and fishing with restrict permits. IUU fishing significantly impacts the stock of target species. Therefore, in this study, the influence of IUU fishing is included in the Species Risk Index (SRI) at the species level, and weights are assigned based on the ratio of the stock, as     ․     . The revised ecosystem-based fisheries assessment method, which considers the impact of IUU fishing, was applied to major fisheries on the south coast of Korea. It is necessary to reduce the non-reporting rate through the expansion of the TAC system and improve the accuracy of statistical compilation. To this end, the electronic fishing reporting system, which is being implemented on all vessels in Korean distant water fishing vessels, should be introduced to the coastal and offshore fisheries as well.

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.