Abstract A right-lateral shear zone in the San-in region, southwest Japan, has been proposed by previous geological and seismological studies. It locates 350 km north of the Nankai Trough, that is, the main plate boundary between the subducting Philippine Sea and overriding Amurian plates and presumably accommodates a part of the relative plate motion. We present a geodetic evidence of the proposed shear zone using GNSS velocity data. Distinct shear deformation is identified only between ~132.5°E and ~135°E along a coastline which is a part of the proposed shear zone, and we propose to call the geodetically identified shear zone as the San-in shear zone (SSZ). The SSZ is a concentrated deformation zone with a width of ~50 km and can be modeled by a deep creep on a vertical strike slip fault with a creep rate of ~5 mm/year. There are some active faults parallel and oblique to the overall trend of the SSZ, but no single active fault coincides with the SSZ. Lineaments of microseismicity and source faults of large earthquakes are almost oriented in NNW–SSE in the SSZ and oblique to the overall trend of the SSZ. They are interpreted as conjugate Riedel shears. Based on these geodetic, seismological, and geomorphological observations, we suggest that the SSZ is a developing and young shear zone in a geological time scale. Graphical Abstract .