The question of whether coseismic ruptures along megasplay faults in accretionary prisms (i.e., large landward-dipping thrust faults branching from the plate boundary) reach the seafloor is critical for assessing the risk of tsunami disaster. However, samples from active megasplay faults have not previously been available. Here we present geochemical and mineralogical data of megasplay fault samples obtained from the shallow (<300 m below seafloor) portion of the megasplay fault that coincides with the rupture area of the A.D. 1944 Tonankai earthquake in the Nankai Trough. The megasplay fault zone is characterized by localized shear zones of brecciated host rocks. A prominent slip zone, here termed “dark gouge,” was discovered within one of the shear zones. Compared to the surrounding breccias, the dark gouge is chemically enriched in Al and K, and depleted in Ca and Sr. It is also characterized by higher illite content in illite-smectite mixed-layer clays. These chemical and mineralogical features may reflect a transformation in clay mineralogy caused by frictional heating, and suggest that the seismic slip can propagate to very shallow levels along megasplay fault systems.