Seismic anisotropy is a useful indicator for identifying the physical and chemical condition of the Earth's interior, such as stress and flow fields, and in situ constituent minerals. Using traveltime tomography, we examined three‐dimensional anisotropic P‐wave velocity structure of the Kii Peninsula, southwest Japan, where source regions of megathrust earthquakes along the Nankai Trough are presumed to exist. The tomography revealed that the Philippine Sea slab beneath the peninsula is segmented, i.e., a high‐velocity slab with E–W anisotropy obtained during seafloor spreading is broken by an anomalous low‐velocity region with N–S anisotropy. The anomaly lies along the segmentation boundary of two previous rupture zones, the 1944 Tonankai and 1946 Nankai earthquakes, and can be explained by the occurrence of a fracture zone with N–S oriented fractures and fault planes revealed by wide‐angle seismic data. It is likely that this anomalous region will form a clear segmentation boundary during future earthquakes.