Southwest Japan lies above an area where the Philippines Sea plate subducts beneath the Eurasian plate. The region experiences relatively high levels of crustal seismicity in addition to the interplate and intraplate seismicity associated with subduction. Crustal earthquakes are common, for example, in the Wakayama district of southwest Japan where they occur as swarmlike seismic activity. Swarm activity is common in volcanic areas but there are no Quaternary volcanic features in the Wakayama district. This report interprets crustal structure in the Wakayama district and its relationship to the swarm activity observed there. We use a new imaging method based on amplitudes of Sp‐converted waves to image the spatial distribution of velocity discontinuities at high resolution. We detected four distinct velocity discontinuities at depths of 2–5, 8–13, 12–22, and 20–27 km. We interpret the 2–5 km discontinuity as the bottom of the sedimentary layer, the 12–22 km feature as the Conrad discontinuity, and the 20–27 km feature as the Moho discontinuity. The 8–13 km velocity discontinuity is detected only beneath the swarm region. The thickness of the upper crust in the swarm region was estimated to be greater than that of surrounding areas. Contrasts in the distribution of velocity discontinuities between the swarm region and surrounding areas suggest that swarm activity is generated by increased pore pressure of fluids escaping from a magmatic body ascending from the mantle.