The Weddell Sea Rift was a major focus for Jurassic extension and magmatism during the early stages of Gondwana break-up and underlies the Weddell Sea Embayment, which separates East Antarctica from a collage of crustal blocks in West Antarctica. Newly-collected aerogeophysical data over the catchments of Institute and Möller ice streams reveal the inland extent of the Weddell Sea Rift against the Ellsworth-Whitmore block and a hitherto unknown major left-lateral strike slip boundary between East and West Antarctica. Aeromagnetic and gravity anomalies define the regional subglacial extent of Proterozoic basement, Middle Cambrian rift-related volcanic rocks, Jurassic intrusions and sedimentary rocks of inferred post-Jurassic age. 2D and 3D magnetic depth-to-source estimates were used to help constrain joint magnetic and gravity models for the region. The models reveal that Proterozoic crust similar to that exposed at Haag Nunataks, extends southeast of the Ellsworth Mountains to the margin of the Coastal Basins. Thick granitic Jurassic intrusions are modelled at the transition between the Ellsworth-Whitmore block and the thinner crust of the Weddell Sea Rift and within the Pagano Shear Zone. The crust beneath the inland extension of the Weddell Sea Rift is modelled as being either ~ 4 km thinner compared to the adjacent Ellsworth-Whitmore block or as underlain by an up to 8 km thick mafic underplate.