We investigated the hypocenter distribution along the Nankai trough off the Kii Peninsula, Japan, by using data from both ocean‐bottom and land‐based seismic networks. Because seismic velocity structures differ greatly below land and ocean, we used a 3D velocity model based on a structural model of the Philippine Sea plate (PHS), which provides much more accurate estimations of source locations than 1D velocity models derived from either onshore or ocean‐bottom seismic data alone, especially for sources between the coast and the trough axis. We identified intensive seismic activity below the axis of the Nankai trough, which we interpreted to be aftershocks of the 2004 Off the Kii Peninsula earthquakes (MJMA 7.1, 7.4, and 6.5), but found much less seismic activity along the subducting PHS. The earthquake sources below the trough axis lie on dipping planes within the PHS, from which we inferred that a fracture zone is developing within the PHS. Our estimated focal mechanisms for these earthquakes showed that their P axes were oriented north–south to northeast–southwest, similar to those of the 2004 events, which were rotated clockwise by 45°–90° from the northwest–southeast direction of convergence between the PHS and the Eurasian plates. We consider that the fracture zone represents a boundary between the PHS and the Izu microplate, which are converging in a north–south direction, and that the 2004 earthquakes and subsequent seismic activity were caused by the collision of these plates.