Stratigraphic and paleontological investigations in Mugi Town, on the Pacific coast of Shikoku Island, revealed evidence of as many as five tsunami inundations from events along the Nankai Trough between 5581 and 3640 cal yr BP. Nine event deposits (E1-E9) were identified in cores ranging in length from 2 to 6 m, consisting of sandy and gravelly layers interbedded with organic-rich mud. Sedimentary structures in the event deposits observed by computed tomography included normal grading and sharp lower stratigraphic contacts. Event deposits E3, E6, E7, and E8 contained mainly brackish-marine diatom species, suggesting that they had been deposited during inundation by seawater. In addition, fossil diatom assemblages were markedly different above and below event deposits E3, E4, E6, and E8. For example, assemblages below event deposit E6 were dominated by a freshwater species (Ulnaria acus), whereas assemblages above it were predominantly brackish-marine (Diploneis smithii, Fallacia forcipata, and Fallacia tenera). We attributed these changes to the increase of marine influence due to coastal subsidence associated with subduction-zone earthquakes, as documented in the 1946 Showa-Nankai earthquakes. We conclude that event deposits E3, E6, and E8 and perhaps E4 and E7 were deposited by tsunamis generated by subduction zone earthquakes along the Nankai Trough. The ages of these event deposits, as constrained by ten radiocarbon ages, suggest that some of the tsunamis that impacted Mugi Town were correlated with those reported elsewhere along the Nankai Trough, thereby complementing the existing but still incomplete geological record for these events.