A self-regulatory community fisheries management program in Korea is designed to enhance fisheries resources, to protect fishing grounds of self-regulatory communities, and to manage their fisheries resources by their own regulations and knowledge. This study explored an applicable ecosystem-based management plan based on the scientific investigation and analysis. This study suggested objectives, indicators and reference points of the ecosystem-based resource management system which are applicable to selfregulatory community fisheries. The objectives of the management system are to maintain sustainable fisheries production, to maintain optimum fishing intensity, to reduce by-catch, to conserve spawning ground and habitat, to maintain optimum habitat environment, to increase/maintain abundance of prey species, to increase/maintain stock biomass, and to conduct stock enhancement on the basis of scientific assessment. The improved methods for the assessment and management are introduced by demonstrating a self-regulatory fishery which targets on hen clam in Dong-li fishing village in Busan.