A sequence stratigraphic study was conducted on the Mendi and Darai Limestone Megasequences in the foreland area of the Papuan Basin in Papuan New Guinea. It involved the integrated use of seismic, wireline log, well core and cuttings, strontium isotope age and biostratigraphic data. This study enhanced the understanding of the structure, stratigraphy and depositional architecture of the limestones, and the morphology of the basin at the time of deposition. The results of the study were integrated with published geological and tectonic models for the Papuan Basin to develop a consistent and coherent model for the depositional history of the limestones. Eleven third-order sequences were delineated within the Mendi and Darai Limestone Megasequences. Eight depositional facies were interpreted across these sequences, namely deep-shelf, shallow-shelf, backreef, reef, shoal, forereef, basin margin and submarine fan facies. Each facies was differentiated according to seismic character and geometry, well core and cuttings descriptions, and its position in the depositional framework of the sequence. Deposition of the Mendi Limestone Megasequence commenced in the Eocene in response to thermal subsidence and eustatic sea-level rise. Sedimentation comprised open-marine, shallow-water, shelfal carbonates. During the middle of the Oligocene, the carbonate shelf was exposed and eroded in response to the collision of the Australian and Pacific Plates, or a major global eustatic sea-level fall. Sedimentation recommenced in the Late Oligocene, however, in response to renewed extensional faulting and subsidence associated with back-arc extension. This marked the onset of deposition of the Darai Limestone Megasequence in the study area. The KFZ, OFZ and Darai Fault were reactivated during this time, resulting in the oblique opening of the Omati Trough. Sedimentation was initially restricted to the Omati Trough and comprised deep and shallow-marine shelfal carbonates. By the Early Miocene, however, movement on the faults had ceased and an extensive carbonate platform had developed across the Gulf of Papua. Carbonate reef growth commenced along topographic highs associated with the KFZ, and led to the establishment of a rimmed carbonate shelf margin. Shallow to locally deeper-marine, shelfal carbonates were deposited on this shelf, and forereef, submarine fan and basin margin carbonates were deposited basinward of the shelf margin. The Uramu High and parts of the Pasca High became submerged during this time and provided sites for pinnacle reef development. During the middle of the Early Miocene, a major global eustatic sea-level fall or flexure of the Papuan Basin associated with Early Miocene ophiolite obduction subaerially exposed the carbonate shelf. This resulted in submarine erosion of the forereef and basin margin sediments. Towards the end of the Early Miocene, however, sedimentation recommenced. Shallow-marine, undifferentiated wackestones and packstones were deposited on the shelf; forereef, submarine fan and basin margin sediments were deposited basinward of the shelf margin; and reef growth recommenced along the shelf margin and on the Pasca and Uramu Highs. By the end of the Early Miocene, however, the pinnacle reef on the Pasca High had drowned. During the middle of the Middle Miocene, subtle inversion associated with ophiolite obduction subaerially exposed the carbonate shelf, and resulted in submarine erosion of the forereef and basin margin sediments. Sedimentation recommenced towards the end of the Middle Miocene, however, in response to eustatic sea-level rise and flexure of the crust associated with foreland basin development. Shallow marine, undifferentiated wackestones, packstones and grainstones were deposited on the shelf; carbonate shoals were deposited along the shelf margin; and forereef, submarine fan and basin margin carbonates were deposited basinward of the shelf margin. Carbonate production rapidly outpaced accommodation space on the shelf during this time, resulting in highstand shedding and the development of a large prograding submarine fan complex basinward of the shelf margin. By the Late Miocene, carbonate deposition had ceased across the majority of the study area in response to a major global eustatic sea-level fall or inversion associated with terrain accreation events along the northern Papuan margin. Minor carbonate deposition continued on parts of the Uramu High, however, until the middle of the Late Miocene. During the latest Miocene, clastic sediments prograded across the carbonate shelf, infilling parts of the foreland basin. Plio-Pleistocene compression resulted in inversion and erosion of the sedimentary package in the northwestern part of the study area. In the southeastern part of the Papuan Basin, however, clastic sedimentation continued to the present day.