Changes in ecosystem risks were evaluated using the ecosystem-based fisheries assessment (EBFA) approach of Zhang et al. (2009, 2010) and the comprehensive ecosystem-based fisheries management (EBFM) plan was made for the southern sea of Korea in this study. The risk assessment of the southern sea ecosystem was conducted by establishing ecosystem management objectives and by estimating risk scores (RS) for indicators. To conduct this analysis a number of indicators and their reference points for assessing these risk scores were developed in this study. The number of indicators in the risk analysis was 28 for the quantitative tier 1 analysis and 30 for the qualitative tier 2 analysis. The objective risk index (ORI), species risk index (SRI) and fisheries risk index (FRI) were calculated from the risk scores. Comparing the past (1988) and the current (2008) status of fisheries resources, management implications were discussed. The fishery risk index (FRI) of large purse seine fishery in the southern sea of Korea decreased substantially from 0.972 in 1988 to 0.883 in 2008, and improvement in the management of fisheries operated in the southern sea of Korea.