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 self-regulatory 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.