Seismic images of the base of the lithosphere across the San Andreas fault system (California, USA) yield new constraints on the distribution of deformation in the deep lithosphere beneath this strike-slip plate boundary. We show that conversions of shear to compressional waves (Sp) across the base of the lithosphere are systematically weaker on the western side of the plate boundary, indicating that the drop in seismic shear-wave velocity from lithosphere to asthenosphere is either smaller or occurs over a larger depth range. In central and northern California, the lithosphere-asthenosphere boundary changes character across a distance of <50 km, and does so directly beneath the San Andreas fault along its simple central segment, and beneath the Calaveras–Green Valley–Bartlett Springs faults to the north. Given the absolute velocities of the North America and Pacific plates, and low viscosities inferred for the asthenosphere, these results indicate the juxtaposition of mantle lithospheres with different properties across these faults. The spatial correlation between the central San Andreas fault and the laterally abrupt change in the velocity structure of the deepest mantle lithosphere points to the accommodation of relative plate motion on a narrow shear zone (<50 km in width), and a rheology that enables strain localization throughout the thickness of the lithosphere.