A dense nationwide seismic network recently constructed in Japan has been yielding large volumes of high-quality data that have made it possible to investigate the seismic structure in the Japanese subduction zone with unprecedented resolution. In this article, recent studies on the subduction of the Philippine Sea and Pacific plates beneath the Japanese Islands and the mechanism of earthquake and magma generation associated with plate subduction are reviewed. Seismic tomographic studies have shown that the Philippine Sea plate subducting beneath southwest Japan is continuous throughout the entire region, from Kanto to Kyushu, without disruption or splitting even beneath the Izu Peninsula as suggested in the past. The contact of the Philippine Sea plate with the Pacific plate subducting below has been found to cause anomalously deep interplate and intraslab earthquake activity in Kanto. Detailed waveform inversion studies have revealed that the asperity model is applicable to interplate earthquakes. Analyses of dense seismic and GPS network data have confirmed the existence of episodic slow slip accompanied in many instances by low-frequency tremors/earthquakes on the plate interface, which are inferred to play an important role in stress loading at asperities. High-resolution studies of the spatial variation of intraslab seismicity and the seismic velocity structure of the slab crust strongly support the dehydration embrittlement hypothesis for the generation of intraslab earthquakes. Seismic tomography studies have shown that water released by dehydration of the slab and secondary convection in the mantle wedge, mechanically induced by slab subduction, are responsible for magma generation in the Japanese islands. Water of slab origin is also inferred to be responsible for large anelastic local deformation of the arc crust leading to inland crustal earthquakes that return the arc crust to a state of spatially uniform deformation.