Java is part of a volcanic island arc situated in the Indonesian archipelago at the southern margin of the Eurasian Plate. Sundaland continental crust, accreted to Eurasia by the Early Mesozoic, now underlies the shallow seas to the north of Java where there has been considerable petroleum exploration. Java has an apparently simple structure in which the east–west physiographic zones identified by van Bemmelen broadly correspond to structural zones. In the north there is the margin of the Sunda Shelf and, in southern Java, there are Cenozoic volcanic arc rocks produced by spatially and temporally discrete episodes of subduction-related volcanism. Between the Sunda Shelf and the volcanic rocks are Cenozoic depocentres of different ages containing sedimentary and volcanic material derived from north and south. This simplicity is complicated by structures inherited from the oldest period of subduction identified beneath Java, in the Cretaceous, by extension related to development of the volcanic arcs, by extension related to development of the Makassar Straits, by late Cenozoic contraction, and by cross-arc extensional faults which are active today. Based on field observations in different parts of Java, we suggest that major thrusting in southern Java has been overlooked. The thrusting has displaced some of the Early Cenozoic volcanic arc rocks northwards by 50 km or more. We suggest Java can be separated into three distinct structural sectors that broadly correspond to the regions of West, Central and East Java. Central Java displays the deepest structural levels of a series of north-directed thrusts, and Cretaceous basement is exposed; the overthrust volcanic arc has been largely removed by erosion. In West and East Java the overthrust volcanic arc is still preserved. In West Java the arc is now thrust onto the shelf sequences that formed on the Sundaland continental margin. In East Java the volcanic arc is thrust onto a thick volcanic/sedimentary sequence formed north of the arc in a flexural basin due largely to volcanic arc loading. All the components required for a petroleum system are present. This hypothesis is yet to be tested by seismic studies and drilling, but, if correct, there may be unexplored petroleum systems in south Java that are worth investigating.