We examined structural changes in the molluscan community for ten years (2001–2010) before and five years (2011–2015) after the 2011 Great East Japan Earthquake and subsequent tsunami around Matsushima Bay, Miyagi Prefecture, northeastern Japan. Before the earthquake and tsunami, Ruditapes philippinarum, Macoma incongrua, Pillucina pisidium, and Batillaria cumingii were dominant, and an alien predator Laguncula pulchella appeared in 2002 and increased in number. After the tsunami, R. philippinarum and M. incongrua populations quickly recovered in 2012, but P. pisidium and B. cumingii populations did not recover until 2015. By contrast, Musculista senhousia, Mya arenaria, Retusa sp., and Solen strictus were found in low densities before the tsunami, but they rapidly increased in abundance/number over five years after the tsunami. These results suggest that the molluscan community on the Tona Coast was drastically changed by the earthquake and tsunami, and some species mainly inhabiting the intertidal—subtidal zone may have increased in number because of land subsidence. We also emphasize that the seawall delayed recovery of the intertidal community after the earthquake and tsunami.