Australia's Coral Sea Marine Park will undergo the most extensive survey of its marine habitats ever, helping scientists to better understand how to protect it, and reef systems like it, across the Pacific.

The park verges the ocean side of the Great Barrier Reef on Australia's Northeast coast, and is home to unique animals and ecosystems, which include black marlin breeding grounds, humpback whale migration paths, and homes for countless other reef dwelling species.

Director of National Parks James Findlay said the project would monitor 20 large reef ecosystems in the coral marine park over the next three years.

"With a management plan coming into effect for the Coral Sea for the first time in July this year, it is very important that we monitor the health of these isolated coral reef ecosystems and increase our understanding of these amazing places."

Scientists will aim to get a better understanding of how the reefs are connected, the impact of coral bleaching, as well as how the reefs recover, which could help in the rehabilitation of other coral systems around the world.

"Our last voyage showed that some reefs have been affected by bleaching, but we saw some signs of recovery," Professor Morgan Pratchett from James Cook University said.

"If no further bleaching occurs, these reefs will continue to recover and may play an important role in the broader recovery of our tropical reef systems."