The 2004 off the Kii Peninsula earthquake occurred on September 5, 2004. Knowing the precise aftershock distribution is important for understanding the mechanism of this earthquake. However, the hypocenter of the main shock was located more than 100 km offshore from the nearest station of the land observation network. In the three days after the main shock, we started ocean bottom seismometer (OBS) observation in order to determine the precise distribution of the aftershocks. We assumed a seismic velocity structure for the hypocenter calculation, based on the results of previous seismic refraction study. The station corrections were incorporated to locate the hypocenter precisely. The hypocenters located within an area covered by five OBSs show relatively small errors. It is found that the OBS-located hypocenters are located about 5.5 km east-southeast from those by JMA and the depth range of the aftershocks is about 5–25 km just beneath the Nankai trough axis. The aftershock hypocenters can be grouped into two clusters at different depths of about 10 km and about 20 km. It is inferred that the main shock also has a depth of 5–25 km. Since this extent of the main shock was larger than one of the oceanic crust of the Philippine Sea plate, the fault plane of the main shock extended at the upper most mantle of the Philippine Sea plate. Although we cannot assign the actual fault plane of the main shock form our observation results, it is clarified that intra-plate earthquakes occurred near the trench region. Our OBS result supports that the main shock was the earthquake not at the plate boundary but within the bending Philippine Sea plate near the trough axis.