The Great Barrier Reef Seabed Biodiversity Project was a $9 million collaboration among four research partners (AIMS, CSIRO, Queensland Department of Primary Industries and Fisheries (QDPI&F), and the Queensland Museum), developed by the CRC Reef partnership with major funding from Fisheries Research and Development Corporation (FRDC), to map non-reef habitats and their biodiversity throughout the Marine Park in depths between 10 and 150 metres. To achieve this, the AIMS flagship RV Lady Basten took collaborators to more than 1,400 locations within a continental shelf area measuring 210,000 km² for benthic surveys using a range of tools including acoustics, cameras, and bottom samplers. This information was pooled with research trawls from almost 450 of the same locations taken by the QDPI&F vessel, FRV Gwendoline May. In the last 12 months, scientists working in laboratories in Townsville, Brisbane, Canberra and Hobart have completed their initial assessment of the samples and turned this information into knowledge about seafloor life.

The result is a comprehensive inventory of distribution and abundance for more than 7,000 species; perhaps four times more than previous data sets. Already, more than 50 species are new to science including fishes, elasmobranchs (sharks and rays), crustaceans and sponges. Many more are known to be new records for Australia and further taxonomic work on the samples (lodged for posterity in the Queensland Museum) are expected to reveal hundreds of others, particularly in less well studied invertebrate groups and algae, adding substantially to the known biodiversity of the Great Barrier Reef.

The scientists also identified key environmental variables likely to be important in structuring seabed distributions including bathymetry, sediment composition, benthic irradiance, current stress, nutrients and turbidity. They developed predictive models for the abundance of each species based on observed relationships with the physical environment, which means that surrogates can be used to predict the abundance of this species in places not yet sampled.

The information has been used to assess conservation goals by informing GBRMPA about the performance of the GBR Zoning Plan (2003), which has met or surpassed the original criterion of preserving at least 20% of each bioregion. It has also been used in preliminary risk analyses of trawl fisheries within the Marine Park to ensure that these industries are conducted in an ecologically sustainable manner, which appears to be the case.

New benthic sled and cod net collects a sample of plants and animals living on the seabed which are used to help identify species recorded on video.