The GIS-based habitat suitability index (HSI) is commonly used to identify the quantitative and qualitative characteristics of habitats. The technique is used to predict species distributions, and assess reserve and management priorities. Habitat suitability index models are useful to estimate the potential distribution of species, particularly in the case of infaunal bivalves. Such index has primarily applied to the benthic stage for commercial species. However, because the life stage of the infaunal bivalves can be largely divided into the planktonic stage and the benthic stage, it is necessary to distinguish the habitate suitability. In this study, the first attempt was made to assess the optimal site by resetting the habitat suitability variables of Manila clams at each life stage. Factors assessed were composed of three: factor Ⅰ is related to the survival of Manila clam at planktonic stage; factor Ⅱ, the growth at benthic stage; factor Ⅲ, environmental condition and relationship with other organisms. In particular, habitat variables related to the growth (chlorophyll “α”, sediment silt-clay), survival (sand classification, hydrodynamics) and environment (dissolved oxygen, salinity) of Manila clams were used in the factor Ⅰ. Factor Ⅱ assessed habitat variables related to the growth (chlorophyll “α”, hydrodynamics), survival (sediment sand, exposure time) and environment (dissolved oxygen, salinity) of Manila clams. The third factor covered the relationship with spatial competition species and the selection of appropriate sites according to the overall tidal flat habitat conditions in regard to habitat management. As a result, the substrate composition and hydrodynamics were considered to have the highest impact on the survival and growth of Manila clams. The optimal site for each research area according to the integrated HSI was found dependent on the characteristics of the habitat of tidal flats. Consequently, it was found that areas which seemed optimal for Manila clam farms covers 9.35 km2 out of 24.4 km2 in Geunso Bay, 9.25 km2 out of 13.1 km2 in Boryeong tidal flat, and 8.82 km2 out of 64.8 km2 in Gomso Bay. It was possible to delineate the preferred habitat and available shellfish farm area for the efficient use and management. Optimal site selection and habitat suitability assessment of involved life stage for Manila clam aquaculture can propose a solution for sustainable use and systematic management in tidal flat.