A new airborne magnetic survey of the southeastern Antarctic Peninsula and adjacent Weddell Sea embayment (WSE) region suggests a continuity of geological structure between the eastern Antarctic Peninsula and the attenuated continental crust of the Filchner Block. This has implications for the reconstructed position of the Ellsworth-Whitmore Mountains block in Gondwana, which is currently uncertain. Palaeomagnetic data indicate that it has migrated from a Palaeozoic position between South Africa and Coats Land to its current position as a microplate embedded in central West Antarctica. The most obvious route for migration is between the Antarctic Peninsula and the Weddell Sea embayment. Evidence that geological structures are continuous across the boundary places constraints on the timing and pathway of migration. Magnetic textures suggest the presence of shallow features extending from the Beaumont Glacier Zone (BGZ) in the west for at least 200 kin into the Weddell Sea embayment. These data suggest that the Eastern Domain of the Antarctic Peninsula and the stretched continental crust of the Filchner Block share a common recent, probably post-Early Jurassic, history. However, examination of deep anomalies indicates differences in the magnetic characteristics of the two blocks. The boundary may mark either the edge of extended continental crust, or a discontinuity between two, once separated, blocks. This discontinuity, or pre-Late Jurassic Antarctic Peninsula terrane boundaries to the west, may have allowed the passage of the Ellsworth-Whitmore Mountains block to its present location.