A re-evaluation of existing onshore and offshore gravity, magnetic, seismic reflection, and well data from the Australo-Antarctic margins suggests that magmatism and along-strike lithospheric heterogeneities have influenced the localization of initial rifting. The 3-D crustal architecture of the Australian and Antarctic margins, which formed during multiple rifting episodes spanning ∼80 Myr, reveal local asymmetries along strike. Rift structures from the broad, late Jurassic (165–145 Ma) rift zone are partially overprinted by a narrower, mid-to-late Cretaceous rift zone (∼100 Ma), which evolved in highly extended crust. This late-stage rift zone is located within a region of heterogeneous crust with faults that cut late syn-rift strata, interpreted as a continent ocean transition zone. This late stage transitional rift is populated by seismically identified rift-parallel basement highs and intracrustal bodies with corresponding positive Bouguer gravity and magnetic anomalies. These undrilled features can be interpreted as exposures of exhumed mantle rocks, lower crustal rocks and/or as discrete magmatic bodies. Our results suggest that strain across an initially broad Australo-Antarctic rift system (165–145 Ma) migrated to a narrow rift zone with some magmatism at 100–83 Ma. Breakup did not occur until ∼53 Ma within the eastern Bight-Wilkes and Otway-Adélie margin sectors, suggesting a west to east propagation of seafloor spreading. The prolonged eastward propagation of seafloor spreading processes and the increased asymmetry of the Australian-Antarctic margins coincides with a change from rift-perpendicular to oblique rifting processes, which in turn coincide with along-strike variations in cratonic to Palaeozoic lithosphere.