We present the first seismic model of the crust beneath Sakhalin based on P and S-wave arrival time data from local earthquakes. Based on the results of numerous synthetic tests, we conclude that this model has fair horizontal and vertical resolution to 20–25 km depth. At shallow depths, seismic anomalies are clearly associated with known geological structures, such as the high-velocity Paleozoic Susunai block and the low-velocity Cenozoic fold belts along the West Sakhalin Mountains. In vertical sections, we observe westward underthrusting of the Susunai block to a distance of at least 70 km, which may represent the regional compression and considerable crustal shortening in this area. Based on the tomography results, we hypothesize about the origin of the mud volcanism in southern Sakhalin. We propose that because of the general westward underthrusting regime in Sakhalin, hydrocarbon-rich shelf sediments may be entrained to considerable depths under the rigid Susunai block, which serves as a nonpermeable cover. The released gases find the weakest zones around the Susunai block and along the Tym-Poronay Fault and escape to the surface to form the South Sakhalin and Lesnovsky mud volcano fields.