The sedimentary basins along the southern Australian and conjugate Antarctic margins formed as a result of Mesozoic rifting. A number of alternative models have been proposed for the pre-rift configuration of Australia and Antarctica. They differ both in how tight the fit between these continents is, and in the lateral juxtaposition of the two continents, ie. some reconstructions place Australia further to the east, relative to a fixed Antarctica, than others. The continuity of comparable geological terranes, surfacemapped shear-zones, and geophysical signatures (e.g. magnetic anomalies) between Australia and Antarctica within Gondwana has implications for assessing these different reconstruction models. To investigate this issue, we tested a range of scenarios for the full-fit configuration of Australia and Antarctica. In the light of palinspastic reconstructions of the extended continental crust within each margin, we investigate how different reconstruction models reconcile geological and geophysical signatures from the conjugate plates. We find that a model that matches the Leeuwin Fracture Zone (in the Australian margin) with the Vincennes Fracture Zone (in the Antarctic margin) reconciles Proterozoic structures previously correlated between the continents based on their geological similarity. These include rocks from the Albany- Fraser orogeny, and the Kalinjala mylonite zone and Mertz shear zones. This model also reconciles the constraints from palinspastic reconstruction of Mesozoic extension better than models that place Australia further east or west relative to Antarctica within Gondwana. This model does not produce a postulated alignment between the Darling Fault in Western Australia and the Denman Glacier in Western Wilkes Land. The preferred fullfit reconstruction model, together with other evidence from the early breakup history between the Australian and Antarctic plates, suggests that the overall opening direction between the two continents was broadly NNW-SSE, but this includes phases of N-S and NW-SE - directed extension.