Australia's shellfish reefs are the country's most threatened ocean ecosystem and are almost extinct.

A study led by The Nature Conservancy, the study found more than 90 per cent of shellfish reefs have disappeared off the nation's coastlines and those remaining are more endangered than the Great Barrier Reef.

A Tasmanian Blenny hides among native flat oysters in an artificial kelp forest off Tasmania. Credit:Cayne Layton

Study leader Dr Chris Gillies says globally, 85 per cent of shellfish reefs, made up of species such as mussels, have been lost or severely damaged, but in Australia, it is "even worse".

"Our study confirms (Australia has) less than one per cent of Flat Oyster and 10 per cent of Rock Oyster habitats remaining," Dr Gillies said.