Halmahera is a K-shaped island located at the junction of several major arc-trench systems of the western Pacific–eastern Indonesia region. Western Halmahera is an active volcanic arc above a zone of intense seismicity which characterizes the north Molucca Sea. Eastern Halmahera has a basement of dismembered ophiolitic rocks with slices of Mesozoic and Eocene sediments overlain unconformably by Middle Oligocene and younger sedimentary and volcanic rocks. The Mesozoic and Eocene sediments reveal notable stratigraphical and petrological similarities to the Marianas fore-arc and the eastern Halmahera Basement Complex is interpreted as a pre-Oligocene fore-arc lacking an accretionary complex. There is some evidence that the pre-Oligocene volcanic arc behind this fore-arc now forms part of the basement of western Halmahera. The Mesozoic and Tertiary sediments were imbricated together with igneous and metamorphic rocks representing the deeper parts of the fore-arc during the Late Eocene plate reorganization event recognized throughout the western Pacific margins. The eastern Halmahera Basement Complex can be traced into eastern Mindanao, probably further northwards in the eastern Philippines and may be related to similar terranes within and around the present Philippine Sea Plate. In contrast, the southern part of the island of Bacan at the southwestern end of the Halmahera group has a basement of continental metamorphic rocks associated with a deformed ophiolitic complex quite different to the basement of eastern Halmahera. The metamorphic rocks are interpreted to be part of the north Australian continental margin basement which is separated from the Halmahera Basement Complex by a splay of the Sorong Fault system and the deformed ophiolite complex of Bacan is suggested to represent magmatism in the fault zone.