Evaluating the habitat suitability of potential aquaculture sites for cultured species is critical to the sustainable use of tidal flats. This study evaluated the habitat suitability index (HSI) of 12 sites in a tidal flat aquaculture farm at Geunso Bay, Taean, in June 2016. The parameters used to model the suitability index were Growth (water temperature, chlorophyll α, hydrodynamics), Survival (sediment-sand, mean size, air exposure), and Environment (DO, salinity). The HSI was calculated using weighted and No weighted geometric means. The results showed high habitat suitability at the bay’s entrance (HIS; No weighted, 0.60-0.70; weighted, 0.60). Hydrodynamics, air exposure, sediment-sand and mean size are thought to have a significant impact on habitat selection by Manila clams Ruditapes philippinarum. This study explored the optimum habitat for Manila clams by calculating the HSI, providing basic data for tidal flat management.