The SE Asian gateway is the connection from the Pacific to the Indian Ocean and it has diminished from a wide ocean to a complex narrow passage with deep barriers (Gordon et al. 2003) as plate movements caused Australia to collide with SE Asia. It is one of several major ocean passages that existed during the Cenozoic but has received much less attention than others that opened, such as the Drake Passage, Tasman Gateway, Arctic Gateway or Bering Straits, or that closed, such as the Panama Gateway or Tethyan Gateway (e.g. von der Heydt & Dijkstra 2006; Lyle et al. 2007, 2008). It is not entirely clear why there has been this comparative neglect, but it may reflect the relative limited knowledge of the large and remote areas of Indonesia and the western Pacific, in particular their geological history, and the relatively small number of active researchers in this large region.

Unlike the Panama Gateway and Tethyan Gateway the SE Asian gateway is still partly open and the ocean currents that flow between the Pacific and Indian Oceans have been the subject of much recent work by oceanographers (e.g. Gordon 2005). We now know that the Indonesian Throughflow, the name given to the waters that pass through the only remaining low latitude oceanic passage on the Earth, plays an important role in Indo-Pacific and global thermohaline flow (Gordon 1986; Godfrey 1996), and it is therefore probable