A three-dimensional upper crustal P wave velocity structure of the Yellowstone region was determined by simultaneous inversion using Pg refracted arrival times and earthquake-generated direct P wave arrival times. The velocity structure was modeled by a two-layer block configuration with the velocity of the surface layer fixed. The inversion was performed on a 14.4-km-thick second layer (5¿6 blocks) using an optimal block size of 21.2¿18.3 km and incorporated the method of separation of parameters. Results show volumes of higher velocities, approximately 6.3 km/s, north of the Yellowstone caldera that correlate with gravity anomaly highs and are interpreted to be associated with near-surface crystalline basement. The upper crust beneath the caldera showed an average velocity of 5.8 km/s with prominent low-velocity zones of 4.9 and 5.2 km/s in the northeast and southwest portions of the caldera, respectively. The 4.9-km/s low-velocity layer in the northeast corner of the caldera coincides with a localized -20-mGal Bouguer gravity low and the largest area of hydrothermal activity in Yellowstone National Park. Relocating earthquakes with the new velocity model showed a systematic migration of epicenters radially toward the caldera by an average of 1.2 km relative to locations using a homogeneous velocity model.