The rupture areas of the large interplate thrust earthquakes along the Nankai trough, offshore southwestern Japan, are divided into several segments. The 1944 Tonankai earthquake ruptured one of the segments off of the Kii Peninsula. In 2005, we conducted an ocean-bottom seismograph experiment at the eastern end of the rupture area of the 1944 earthquake. Little seismic activity was observed on the plate interface; most earthquake activity was within the subducting and overriding plates. Aftershocks of the 2004 off Kii Peninsula earthquake, which was an intraplate earthquake in the subducting Philippine Sea plate, were mainly located in the subducting oceanic crust and uppermost mantle. However, several earthquakes at the eastern end of the rupture area of the 1944 earthquake were in the sedimentary wedge, with a focal mechanism indicating deformation by a subducting seamount. The earthquakes and faults in the sedimentary wedge show deformation related to the irregular topography of the subducting oceanic crust to the east of the rupture area of the 1944 Tonankai earthquake. In contrast, few earthquakes were observed in the sedimentary wedge in the rupture area of the 1944 earthquake. Difference in topography of the subducting oceanic crust in the two areas might have caused spatial variations of interplate coupling, which, in turn, caused the observed differences in the deformation of the sedimentary wedge. The spatial variation of interplate coupling may affect rupture propagation during large interplate earthquakes and cause the segmentation of large interplate earthquakes along the Nankai trough.