Recent heat flow surveys in the Japan Trench and Nankai Trough areas delineate prominent heat flow anomalies correlated with the structure of the subducting oceanic crust. On the seaward side of the Japan Trench, anomalously high heat flow values are pervasively observed within 150 km of the trench axis. The broad high heat flow zone can be attributed to trenchward thickening of a permeable layer (aquifer) in the oceanic crust associated with fracturing due to plate bending. Fluid circulation in the thickening aquifer efficiently pumps heat up from the underlying unfractured part. Overlapping the broad anomaly, local variations at a scale of a few kilometers are detected, indicating heterogeneous development of fractures. On the floor of the Nankai Trough off the Kii Peninsula, observed heat flow varies from extremely high and variable values on the western side to normal values for the seafloor age on the eastern side. The transition occurs at around 136°E, which may correspond to the structural boundary in the Shikoku Basin between the seafloor formed by spreading in the NE–SW direction and that formed by spreading in the E–W direction. The high heat flow west of the boundary is considered to result from heat transport along the plate interface by fluid circulation in an aquifer in the subducted oceanic crust. The heat flow transition around 136°E may reflect a change in permeability structure across the boundary between the two spreading directions. The two types of hydrothermal heat transport, fluid circulation in the subducted aquifer in the case of the Nankai Trough and circulation in the thickening aquifer in the case of the Japan Trench, have distinctive features. The subducted-aquifer type is effective for heat transport in a young subducting plate with a highly permeable aquifer, while the thickening-aquifer type can transport heat even in an old plate. The subducted-aquifer type has a more significant influence on the temperature structure of the plate boundary. Some heat flow anomalies observed in other trenches may also be caused by either of these types of hydrothermal heat transport.