We use over 8000 regional and local earthquakes and ∼150,000 seismic arrivals recorded by a dense broadband seismic network in the St. Elias region, southern Alaska, and nearby regional stations to compute the 3D velocity structure down to a depth of ∼80 km. The tectonics of this region is dominated by a collision between the subducting Yakutat microplate and the North American continent. This model reveals slower velocities along the northern edge of the Yakutat microplate in the St. Elias coastal range that can be traced as deep as 30 km. This velocity anomaly contrasts with the offshore area in the south and the region north of the Chugach–St. Elias and Bagley faults and corresponds to tectonically off‐scraped and deformed rocks of the Yakutat sedimentary cover. The Chugach–St. Elias fault serves as a back stop for the deformed Yakutat sediments rather than the Bagley fault and represents a prominent structural boundary east of the Pamplona fault zone. The northward dipping Yakutat basement is imaged at depth and extends toward the Wrangell volcanoes. The region between the Bagley fault and the Wrangell volcanic field is characterized by higher crustal velocities, whereas the Wrangell volcanic field is characterized by slower velocities both near the surface and at depth. A strong low‐velocity anomaly corresponding to the Copper River sedimentary basin can be traced down to 20 km depth.