The Oldest Ice Reconnaissance (OIR) airborne geophysical survey in East Antarctica was flown over approximately 170,000 km2 of the Dome Fuji region in 2016/17. The survey’s results support new insights into the subglacial geology and its meaning for the tectonic histories of the supercontinents Rodinia and Gondwana. The new magnetic and radar-derived bed topography data are integrated with previously acquired magnetic and gravity data, allowing the mapping of crustal domains within and beyond the survey’s limits. The magnetic data reveal three distinct domains within the survey region, delineated by N–S oriented boundaries, partly aligned with gravity domains following upward continuation transformations for both datasets. Additionally, four primary sets of magnetic lineaments were identified, exhibiting correlations with topographic and gravity patterns. These correlations indicate the continuation of the Tonian Oceanic Arc Super Terrane (TOAST) southward of its previously known southern limit. Moreover, an E–W-trending magnetic anomaly, the Elbert magnetic anomaly, suggests the suture between the recently-proposed subglacial Valkyrie craton and the TOAST. Furthermore, the analysis reveals a broad scale shear zone, named here the OIR shear zone, which formed as a result of oblique collision of the Ruker and Valkyrie cratons during the amalgamation of Gondwana.