Abstract We present a synthesis based on the interpretation of two pairs of deep seismic reflection crustal sections within the Southern Rift System (SRS) separating Australia and Antarctica. One pair of sections is from the conjugate margins between the Great Australian Bight (GAB) and Wilkes Land, in the central sector of the SRS, which broke up in the Campanian. The second pair of conjugate sections is located approximately 400 km further east, between the Otway Basin and Terre Adélie, which probably broke up in Maastrichtian time. Interpretations are based on an integrated synthesis of deep multi-channel seismic, gravity and magnetic data, together with sparse sonobuoy and dredging information, and the conjugate sections are presented with the oceanic crust removed beyond the continent–ocean boundary (COB). At first order, both conjugate pairs show a transition from thinned continental crust, through a wide and internally complex continent–ocean transition zone (COTZ), which shows features in common with magma-poor rifted margins worldwide, such as basement ridges interpreted as exhumed subcontinental mantle. In the central GAB sector, the COTZ is symmetric around the point of break-up and displays a pair of mantle ridges, one on each margin, outboard of which lies a deep-water rift basin. Break-up has occurred in the centre of this basin in this sector of the SRS. In contrast, the Terre Adélie margin is nearly 600 km wide and shows an abandoned crustal megaboudin, the Adélie Rift Block. This block is underlain by interpreted middle crust, and appears to have a mantle ridge structure inboard, as well as an outboard exhumed mantle complex from which mylonitized harzburgite has been dredged. The conjugate margin of the Beachport Sub-basin is relatively narrow ( c. 100 km wide) and does not appear to contain an exhumed mantle ridge, as observed along strike in the GAB. These observations from a single rift spreading compartment show that radically different break-up symmetries and margin architectures can result from an essentially symmetric rifting process involving multiple, paired detachment systems. This indicates the need for caution in interpreting causative mechanisms of rifting from limited conjugate sections in other rifts. We speculate that the underlying crustal composition, rheology and structural preconditioning play a significant role in partitioning strain during the transition to break-up.