The marine Drug Discovery Project conducted two major collections in Commonwealth waters of the Indian Ocean, from shallow in-shore sites to deep water sites to pristine reefs of the North-West Shelf. Each of these sites has been chosen to increase the diverstiy of the collection and enhance the likelihood of discoveing molecules beneficial to medicine. The trips have involved staff from AIMS and the Western Australian and Northern Territory Museums, each of which collected their own samples. A wide range of marine organisms, from bacteria to sponges, have been collected, with each collecting trip yielding several hundred organisms for extraction. These extracts, each containing hundreds of natural products, are screened for activity against various human diseases and disorders. Extracts from these collections have been processed and prioritised for the isolation of target bioactive molecules.