Indonesia is positioned at the nexus of two oceans. Its diverse deep-sea habitats include migration corridors, seamounts, canyons, trenches and upwelling zones that are of regional importance within the Indo-Pacific, yet remain poorly known. From 1998-2011 visual and acoustic surveys and research have been conducted on blue whales, sperm whales and other oceanic cetaceans. Outcomes have been instrumental to a) identify critical deep-sea habitats for large cetaceans and other migratory megafauna b) support MPA Network design and c) develop ocean management policy for offshore industries (oil and gas, shipping) in Indonesia and the Coral Triangle.The Lesser Sunda ecoregion mapping project categorized 13 distinct deep-sea habitat types. Ecological and human use characteristics were evaluated for all identified sites. Due to the extreme depth gradients, numerous seamounts and persistent pelagic habitats were located near-shore. There is a clear opportunity to improve the protective management for these deep-sea yet near-shore habitats. Simultaneously, technological advances have allowed a rapid expansion of pelagic fisheries and a boom in oil and gas activities in deep waters. Regional shipping is estimated to increase significantly, especially along major international sea lanes which overlap with migration corridors.
Currently, deep-sea habitats are vastly under-represented in policy development and MPA Networks throughout the Coral Triangle. This marine conservation gap is slowly being addressed. The design of the Raja Ampat , Savu Sea and Kimbe Bay MPAs specifically included canyons, corridors and seamounts. Conservation measures for associated oceanic megafauna are being implemented. In addition, best practices have been developed for seismic surveys (ocean noise) in the bio-diverse waters of the Coral Triangle. These new developments will be relevant to other archipelagic nations such as the Philippines, Papua New Guinea and the Solomon Islands.