Collision between Australia and SE Asia began in the Early Miocene and reduced the former wide ocean between them to a complex passage which connects the Pacific and Indian Oceans. Today, the Indonesian Throughflow passes through this gateway and plays an important role in global thermohaline flow. The surrounding region contains the maximum global diversity for many marine and terrestrial organisms. Reconstruction of this geologically complex region is essential for understanding its role in oceanic and atmospheric circulation, climate impacts, and the origin of its biodiversity. The papers in this volume discuss the Palaeozoic to Cenozoic geological background to Australia and SE Asia collision. They provide the background for accounts of the modern Indonesian Throughflow and oceanographic changes since the Neogene, and consider aspects of the region's climate history.