Tsunamis are huge disasters that can significantly damage benthic organisms and the sea-bottom environment in coastal areas. It is of great ecological importance to understand how benthic ecosystems respond to such destructive forces and how individual species are affected. Investigating the effect of such disasters on animals that are seldom caught alive is particularly difficult. Bivalve mollusks are especially suitable for investigating how a tsunami affects coastal benthic species because they preserve an environmental record in their shells that can be extended back in time by crossdating the records of multiple individuals. Here we studied dead shells of Mercenaria stimpsoni, a long-lived clam, and precisely determined the time of death by using nuclear bomb–induced radiocarbon (bomb-14C) and by counting annual growth increments. First, a quasi-continuous, regional bomb-14C record was created by analyzing the shells of 6 live-caught M. stimpsoni individuals. Then 27 dead shells collected from the seafloor of Funakoshi Bay were 14C-dated and analyzed. The results showed that the huge tsunami that struck northeastern Japan on 11 March 2011 caused mass mortality of this bivalve in Funakoshi Bay. Nine of the 27 clams died during the March 2011 tsunami, probably by starvation after burial by tsunami deposits or exposure above the seafloor as a result of sediment liquefaction during the earthquake. The dating method used in this study can help us understand how long-lived marine organisms with low population density are affected by huge natural disasters such as a tsunami.