Concern is growing over how ecosystems are being affected by fishing. A comprehensive ecosystem-based approach is required to holistically assess and manage fisheries resources and their associated habitats by considering ecological interactions of target species with predators, competitors, and prey species, interactions between fishes and their habitats, and the effects of fishing on these processes. A pragmatic ecosystem-based approach was developed for the assessment of fisheries resources in Korean waters involving three management objectives: sustainability, biodiversity, and habitat quality. A two-tier analytical method was employed. Tier 1 was designed for situations where sufficient information is available to allow for a quantitative evaluation of the status of the system, while Tier 2 was designed for situations where available information necessitated a semi-quantitative or qualitative assessment. A total of 20 Tier 1 indicators and 24 Tier 2 indicators were developed for assessment of ecosystem status. Both target and limit reference points were chosen for each indicator to assess the status of species, fisheries and ecosystems. Nested risk indices, such as objectives risk index (ORI), species risk index (SRI), fishery risk index (FRI), and ecosystem risk index (ERI), were developed to assess the ecosystem status at the management unit level. A risk assessment diagram was developed and found to be useful in quickly displaying results. A management status index (MSI) was also developed to evaluate the level of management improvement in species, fisheries, or ecosystems among different time periods or different areas. The method was demonstrated by applying it to the Tongyeong marine ranch and the Korean large purse seine fishery. It was found that this approach can be used to compare the status of species, fisheries and ecosystems spatially and temporally using an ecosystem perspective.