Four ancient tsunami deposits were identified in a trench excavated on Ishigaki Island, Okinawa, Japan. Three of the tsunami deposits (T-I, T-II, and T-IV) consist of calcareous sand beds, whereas the other (T-III, located stratigraphically between T-II and T-IV) consists of boulders. Deposit T-I was caused by a tsunami in 1771.14 C dating, together with the elevations of the landward margins of these sandy tsunami deposits, suggests that tsunamis II and IV were similar in size to the 1771 tsunami, although the influence of local topographic features on the magnitudes of tsunamis has not yet been examined. This study reconstructs the local topographic features by comparing the molluscan assemblages incorporated within the tsunami deposits with those in recent beach deposits. The presence of species that inhabit the intertidal zone in lagoonal settings in all the assemblages indicates that the present-day shallow lagoon has been present off the study area since the occurrence of tsunami T-IV, which supports the previous hypothesis that the magnitudes of the 1771 tsunami and tsunamis II and IV were similar. These molluscan assemblages also suggest that a high relative abundance of large, heavy mollusc shells is a feature of the paleotsunami deposits in the coastal lowlands found along the shallow coral lagoons.