Measurements of the seafloor deformation under ocean waves (compliance) reveal an asymmetric lower crustal partial melt zone (shear velocity less than 1.8 km/s) beneath the East Pacific Rise axis between 9° and 10°N. At 9°48′N, the zone is less than 8 km wide and is centered beneath the rise axis. The zone shifts west of the rise axis as the rise approaches the westward-stepping 9°N overlapping spreading center discontinuity and is anomalously wide at the northern tip of the discontinuity. The ratio of the compliance determined shear velocity to the compressional velocities (estimated by seismic tomography) suggests that the melt is well-connected in high-aspect ratio cracks rather than in isolated sills. The shear and compressional velocities indicate less than 18% melt in the lower crust on average. The compliance measurements also reveal a separate lower crustal partial melt zone 10 km east of the rise axis at 9°48′N and isolated melt bodies near the Moho beneath four of the 39 measurement sites (three on-axis and one off-axis). The offset of the central melt zone from the rise axis correlates strongly with the offset of the overlying axial melt lens and the inferred center of mantle melting, but its shape appears to be controlled by crustal processes.