Most of Korean farms have been developed in the semi-closed bay, and its position is very vulnerable to the coastal contamination due to the long term and the high density. So, mariculture management is very essential for the sustainable aquaculture. Some of the specific ways would be the assessment of the optimal stocking density for mariculture management zone and this has to consider both the suitable site selection and the assessment of ecological carrying capacity. Habitat suitability index(0.0 totally unsuitable habitat, 1.0 optimum habitat) and ecological indicator(Filtration pressure indicator) was used to assess the stocking density for oyster farms in Geoje-Hansan Bay. Geoje Bay showed the higher habitat suitability index value 0.75 than Hansan Bay 0.53, indicating that Geoje Bay is more suitable for oyster farming. Ecological indicator showed different stocking density according to the coastal characteristics in Geoje-Hansan Bay. Consequently, it is desirable that the stocking density in Geoje Bay should reduce average 40% and Hansan Bay, average 60% than present, in order to meet the ecological carrying capacity. The assessment of the stocking density could solve various problems such as the coastal contamination, environmental aggravation and the productivity decrease and this study could be a scientific basis to establish the policies for mariculture management.