Three‐dimensional, in situ stresses in the Kumano Basin and slope sediment (IODP Sites C0002 and C0022) in the Nankai Trough, southwest Japan, have been determined using the anelastic strain recovery (ASR) of core samples. Two samples taken from Hole C0002J, located in the bottom of the Kumano Basin, indicate that the maximum principal stress, σ1, is vertical. The intermediate principal stress, σ2, is oriented ENE–WSW, parallel to the trench axis. These stress orientations are similar to those obtained using ASR and borehole breakout methods in previous expeditions. In contrast, a sample from the lower section of the slope sediment (Hole C0022B), located beneath the megasplay fault, is characterized by σ1 plunging moderately to the ESE and σ3 oriented near‐horizontally, trending NNE–SSW. The direction of maximum horizontal stress obtained from ASR (WNW–ESE) is similar to that inferred from borehole breakouts in an adjacent hole (NW–SE). Trench‐normal compression and a near‐vertical σ2 are also inferred from focal mechanisms of very‐low‐frequency earthquakes within the Nankai accretionary prism, and from borehole breakouts in the hanging wall of the megasplay fault. These observations suggest that the horizontal compressional regime extends to a shallower level than previously thought, likely due to the shallow portion of the megasplay fault accumulating tectonic stress in response to plate convergence.