The potential of ecosystem-based fisheries management is recently recognized to be very important to improve the sustainability of fisheries resources. Under the depressed condition of many fisheries resources, this recognition has been expanded and more effort has been taken to improve this approach. Taking ecosystem concept includes the use of other tools of management in addition to fisheries regulation, such as stock and productivity enhancement, provision of physical structure, or marine protected areas. In the ecosystem-based fisheries management approach, it would require to holistically consider ecological interactions of target species with predators, competitors, and prey species, the effects of climate on fisheries ecology, the complex interactions between fishes and their habitat, and the effects of fishing on fish stocks and their ecosystem. Fisheries management based upon the understanding of these factors can prevent significant and potentially irreversible changes in marine ecosystems caused by fishing. A useful approach for analyzing tropho-dynamic interactions and mass-balance in marine ecosystems is introduced to demonstrate the complexity and usefulness of the ecosystem approach, which was applied to a small ecosystem in Korea. Korea should seriously consider to take the ecosystem-based approach to fisheries management, since most major fish stocks are currently depleted due to many reasons such as overfishing, land reclamation and coastal pollution.