Interpretation of deep seismic reflection profiling, coupled with forward modelling of gravity and aeromagnetic data, new zircon U-Pb dating and the interpretation of the basement geology beneath the southern margin of the Eromanga Basin, has provided insights into the southern part of the underlying Thomson Orogen and its relationship with the Lachlan Orogen to the south. Our interpretations of these data suggest that the northern Lachlan and southern Thomson orogens had a shared history from the mid-Silurian to the Carboniferous. Major older differences, however, are suggested by the presence in the southern Thomson Orogen of: (i) a possible Neoproterozoic arc, (ii) latest Cambrian to earliest Ordovician turbidites, (iii) Late Ordovician turbidites, and (iv) geophysical evidence for thrusting of reflective ocean crust rocks high into the crust on a north-dipping detachment. The seismically imaged, north-dipping, crustal-scale Olepoloko Fault corresponds to the 'surface expression' of the Thomson-Lachlan boundary. We speculate that it reflects the partial reactivation and short-cutting of an older fault in the post-Devonian (?Carboniferous) and probably also in the latest Silurian and Early Devonian. Comparisons with the seismic architecture of the Lachlan Orogen immediately to the south, and with the central part of the Thomson Orogen ∼450 and 650 km to the north, suggest that the part of the Thomson Orogen west of the Quilpie Trough and the Nebine Ridge developed on inferred Neoproterozoic to Cambrian oceanic crust that floors the Barcoo Basin. This basin separated the continental margin at that time on the west from a sliver of continental crust preserved at Anakie on the east that was overlain by one or more, poorly dated, passive margin sedimentary ± volcanic sequences that predate a 500 Ma deformation. The southern margin of the Thomson Orogen also contains a sliver of old continental crust, sandwiched between the southern strike-slip margin of the Barcoo Basin to the north and the open proto-Pacific ocean to the south. It was locally the site of ca 580 Ma subduction, because seafloor spreading to the south lay oblique to the orogen margin. We suggest that the Thomson Orogen and Lachlan Orogen were amalgamated by the late Middle Ordovician, although the Thomson-Lachlan boundary remained a zone of weakness at least until the Triassic.