Detailed analyses of cores from two drill sites landward of the Nankai trough provide constraints on the evolution of stress across the SW Japan subduction zone. Core-scale faults at Sites C0001 and C0002 suggest changing stress geometries that shed light on mechanical coupling across this plate boundary. Normal faults dominate the record of brittle strain in both the sedimentary cover and the upper accretionary prism, and these cut older shear zones and vein structures. Based on cross-cutting relations normal faults postdate thrust faults with the latter interpreted to be inactive. The normal faults, in contrast, are consistent with contemporary stress proxies such as borehole breakout and anelastic strain recovery data. Stress inversion for faults that are restored to original orientations using paleomagnetic data reveal that thrusting has accommodated trench subperpendicular shortening associated with interplate coupling. This phase of deformation is overprinted by normal faulting attributed to mechanical decoupling of the upper plate from the lower plate in response to the underplating of anomalously weak sediments between an out-of-sequence thrust and the décollement. These observations suggest that core-scale faults record a stress history that is, to date, not apparent from in situ stress proxies such as borehole breakout data or anelastic strain recovery data. We conclude that the brittle faults provide a unique record of changing stress conditions that can be recognized only through coring.