The Late Palaeogene–Quaternary stratigraphy of Halmahera is described, and new formation names are proposed, based on recent field investigations of the NE and central part of the island. This stratigraphic information provides new insights into the Neogene history of Halmahera and the development of the present island arc. The Late Palaeogene and younger rocks rest unconformably on an ophiolitic Basement Complex which formed part of a Late Cretaceous–Early Tertiary fore-arc. After volcanic arc activity ceased in the Eocene the former fore-arc terrane was uplifted and deeply eroded in the Late Palaeogene. Some of the Late Palaeogene–Early Miocene river valleys are currently being re-excavated by the present rivers. Slow subsidence began in the mid–late Oligocene and by the end of the Miocene all eastern Halmahera was the site of shallow-water carbonate deposition. There is no evidence for arc volcanism in central Halmahera at this time and the reported Oligo-Miocene volcanism in nearby regions is interpreted as volcanism related to the Sorong Fault system. The Miocene shallow water region subsided rapidly in the Early Pliocene and the sedimentary basin formed was filled with marls succeeded by siliciclastic turbidites, with increasing amounts of calc-alkaline volcanic debris from a Pliocene volcanic arc built on the western arms of Halmahera, probably on the eroded Early Tertiary arc. This phase of rapid subsidence in the Pliocene back-arc region resulted from the initiation of subduction of the Molucca Sea lithosphere eastwards beneath Halmahera. Differential subsidence on NW–SE and NE–SW sets of faults in the region immediately behind the active arc led to the formation of deep sediment-filled basins adjacent to the eastern arms. A major deformation event in the Pleistocene resulted in folding and local thrusting at the junction between eastern and western Halmahera and volcanism ceased in the Pliocene arc. The third Halmahera arc, the Quaternary arc, currently active in the northern part of the islands, began activity within the last 1 Ma and is built upon the deformed and partly eroded Pliocene arc. The Pleistocene deformation event and shift in position of the arc are interpreted as the result of the interaction of the eastward-dipping Molucca Sea plate with adjacent plates, either with a fragment of the Australian continent in the Sorong Fault zone and/or with the Philippine Sea plate beneath northern Halmahera.