In East Timor the upper parts of the Permian to Middle Jurassic Gondwana Megasequence are structurally juxtaposed against indurated carbonate pelagites of Early Cretaceous (Aptian) to early Late Miocene age. The pelagites probably represent a thin (several hundred metres thick) succession that was deposited at middle to lower bathyal water depths unconformably above the Gondwana succession after continental breakup. The widespread occurrence of pelagites, lack of turbidites at least in the post-Albian succession, association with upper parts of the Gondwana Megasequence and with Upper Jurassic shales of Australian affinity, and stratigraphic correspondence with adjacent Australian basins suggest that these sediments were deposited on a middle bathyal continental terrace similar to the present-day Exmouth Plateau. Evidence of chaotic soft-sediment mixing affecting units as young as early Late Miocene and analogy to present-day coeval successions on undeformed continental terraces suggest that the carbonate pelagites were friable chalk or ooze prior to deformation. Cementation, stylolitisation, and vein formation took place after the early Late Miocene (i.e. after 10.9-9.8 Ma GTS2004). Overlying the deformed succession is the Pliocene-Pleistocene Viqueque Megasequence (planktonic foraminiferal Zones N18-N23) with a thin basal unit of friable chalk (30 m thick in the type area) that was deposited at middle to lower bathyal water depths similar to the older carbonate pelagites. The basal chalk ranges from zone N18 through N20 (Early to Middle Pliocene) and suggests a quiet tectonic interval, although the first indication of distal turbiditic deposition, presumably to the north, lies in the 4.2-3.35 Ma GTS2004 interval. Proximal turbidite deposition commenced at around 3.35 Ma GTS2004 with clasts sourced from an emerging Timor island to the north. The basal unit of the Viqueque Megasequence together with the older carbonate pelagite succession suggests that a middle bathyal continental terrace setting continued in this region, at least on the southern side of Timor, from the Cretaceous - Paleogene to the Late Miocene and Early Pliocene. The soft-sediment mixing, probably induced by tectonism, in the deformed pelagites, and the Bobonaro Melange beneath the relatively undeformed type section of the Viqueque Megasequence suggest that during part of the Late Miocene (9.8-5.6 Ma GTS2004), tectonic mobilisation of sedimentary units took place, and mud volcanoes erupted on the seafloor. The Timor highlands were emergent from about 3.35 Ma GTS2004 (Middle Pliocene) as the deformation front moved from the north. The Timor Trough developed as a gentle downwarp from a pre-existing continental terrace that had been located in the middle bathyal zone since the late Early Cretaceous.