Continental fragments with Australian/Gondwanan stratigraphic affinities are widely distributed throughout the eastern Indonesia collision complex. Despite t heir structural isolation from one another as a consequence of Tertiary orogenesis, these fragments show a remarkably uniform pattern of Permo-Triassic tectonostratigraphy, ranging from a granitoid belt in the north, through a continental platform, to an intracontinental rift system in the south. Within the rift system complementary upper and lower plate rifted margins can be recognised in the northern and southern Banda Arcs, respectively. The northern granitoid belt was initiated in the mid-Carboniferous, whilst the intracontinental rift system began to develop in latest Carboniferous-earliest Permian times. Extension in the northern rift margin ceased in the mid-Camian (early Late Triassic), contemporaneous with a marked decline in igneous activity in the granitoid belt to the north. The Sibumasu Terrane of mainland SE Asia probably originated on the Gondwanaland continental margin, adjacent to reconstructed eastern Indonesia, but rifted away during the Early Permian. Previous interpretations have seen this rifting as marking the final separation between Gondwanaland and continental terranes now forming SE Asia. Alternatively, it is suggested here that Gondwanan eastern Indonesia acted as an indirect continental connection between Sibumasu/Indochina and Australia during the Permian and Triassic. This continental isthmus permitted continuing limited floral and faunal interchange between Gondwanaland and SE Asia until a final separation in the Late Triassic. The mid-Carnian structural event in eastern Indonesia is interpreted as related to this separation. (C) 2001 Elsevier Science Ltd. All rights reserved.