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During the Late Tertiary, Irian Jayan fold and thrust belts were uplifted whilst subsidence and sedimentation took place in nearby basins. Uplift occurred in two separate phases, and polyphase folds have been identified in the zone of interaction between the Central Thrust Belt and the Lengguru Fold Belt. The older structures formed ahead of oceanic crustal slabs, during obduction onto the northern margin of the Australian Plate. The younger structures formed after oceanic obduction ceased, and since the Late Pliocene. Folds and thrusts are controlled by restraining bends in a NE-SW trending dextral, transcurrent fault system. Extensional basins probably formed along releasing bends in the same fault system, which is conjugate to the active sinistral Sorong and Tarera Faults.The presence of two generations of structure in the thrust belts has implications for hydrocarbon trap prospectivity. If hydrocarbon generation is presumed to have ceased during the earlier uplift phase, structural traps formed prior to final cessation of generation are lower risk with regard to primary hydrocarbon charge. Younger structures, formed well after generation ceased, must rely on secondary migration for charge and therefore represent a higher risk group of traps.Two distinct age groups of compressive structures can also be recognised in the Papuan Thrust Belt, but they have formed ahead of discrete accreted terranes, which only overlap along a narrow zone. Consequently, in most parts of the Thrust Belt, only one generation of fold is present. In PNG, the plate-bounding, transcurrent fault systems lie well to the north of the Thrust Belt, and any deformation related to their displacement probably affects only the Northern Papuan basins. Significantly, within the Thrust Belt, hydrocarbons have been discovered in both the older and younger generations of trap.