Oceanic crust formed at mid-ocean ridges may be later modified by off-ridge magmatism forming seamounts, guyots, and islands. We investigate processes associated with seamount formation in the Gulf of Alaska Seamount Province using two coincident seismic reflection/wide-angle profiles. A north-south profile crosses the Kodiak-Bowie Seamount Chain and Aja fracture zone (FZ), and an orthogonal east-west profile is located about 90 km south of the seamount chain over Pacific plate oceanic crust. Structure along the profile away from the seamount chain is consistent with typical oceanic crust. Crust in our study region is thinnest (about 5.6 km) at the Aja FZ. Unlike observations from active transform faults, no low-velocity anomaly is observed at the Aja FZ suggesting that the crustal velocities have recovered to normal values through crack closure and crack healing. Higher lower crustal velocities (∼7.3 and > 7.5 km/s) and thicker crust (∼8.5 and ∼7.0 km) are observed near the Pratt and Durgin Seamounts and at the intersection of the Kodiak-Bowie Seamount Chain linear trend, respectively. These observations are attributed to magmatic underplating associated with seamount province magmatism. Lithospheric thickness variations across the Aja FZ may form a barrier or impediment to magmatic flow. The thickest crust (8.5 km) along our two profiles is located on the younger side of the FZ, and we suggest that the majority of magmatism jumped south of the Aja FZ when thinner lithosphere was encountered by the Bowie hot spot. The crustal structure near the Kodiak-Bowie Seamount Chain is most similar to that of other seamounts and guyots that formed on similarly young lithosphere (8–12 Ma). Our results suggest that lithospheric thickness at the time of hot spot interaction has a large control on magmatic underplating at seamounts and seamount provinces.