Corals at Ishigaki Island, Japan, are characterized by their high species diversity. Not only are they struck by storm waves generated annually by typhoons, the corals, especially the massive ones, in the fringing reef were buffeted by huge tsunami waves with a run-up height of ca. 30 m in 1771 Meiwa tsunami and its predecessors at few hundredyear intervals. We present field survey and numerical results demonstrating that such near-field large tsunamis could have reset the growth of massive corals, a phenomenon which large typhoons have not caused. Our field survey revealed that the massive corals in the lagoon are not attached to the bedrock but are instead located on the sandy sea bottom. Therefore, those are movable of sufficiently large wave inundated in the lagoon. Our numerical results further showed that the maximum velocity of the tsunami at the reef edge, calculable as < 21.2 m/s at the study area, is still high in the shallow lagoon, perhaps generating sufficiently strong hydrodynamic force to devastate the massive corals in the shallow lagoon entirely, as well as some presumed damages on tabular and branching corals on the reef crest and reef slope. This numerical result is consistent with the observed fact that even a 9-m long Porites boulder (about 220 t) was cast ashore by the 1771 tsunami. The sizes of the presently living massive corals of Porites spp. are consistent with our hypothesis that they started to grow after the latest 1771 tsunami event. At the coral reefs of high tsunami-risk countries, severe destruction of corals by large tsunami waves should be considered for their growth history because, depending on the bathymetry, coral characteristics, and tsunami hydrodynamic features, tsunamis can radically alter coral habitats.