The Great Barrier Reef Marine Park Authority works closely with international, national, state and local agencies in the conservation and protection of biodiversity.

A protected species is a plant or animal that is protected by law and needs special management. Species may be protected at an international, national, state or local level:

• International level: species that are listed as vulnerable, endangered or critically endangered under IUCN (World Conservation Union) Red Data Book.
• National level: species that are a listed threatened species, a listed migratory species or a listed marine species under the Environment Protection and Biodiversity Conservation Act 1999
• State level: species of marine mammal, bird or reptile that are prescribed as endangered, vulnerable, near threatened and least concern under the Nature Conservation Act 1992 of Queensland
• Local level: species mentioned in Table 29 of the Great Barrier Reef Marine Park Regulations 1983.

In addition, protected species in the Great Barrier Reef are classified as either threatened, iconic or at risk:

1. A protected species is classified as 'threatened' if its population has declined within and adjacent to the Great Barrier Reef
2. A protected species is classified as 'iconic' if it is one of Australia’s most well-known plants or animals and requires special management in the Great Barrier Reef Marine Park
3. A protected species is classified as 'at risk' if it faces pressure from human-related pressure activities within and adjacent to the Great Barrier Reef.

The list of protected species for the Great Barrier Reef Marine Park includes:

• Some shells - helmet shells, triton shells, tridacnid clams
• Some fish - seahorses, pipefish, sea dragons, potato cod, Queensland grouper, barramundi cod, Maori wrasse, all groupers (Epinephelus) more than 100 cm
• Some sharks - whale shark, grey nurse shark, great white shark, freshwater and green sawfish
• Sea snakes
• Crocodiles
• Marine turtles
• Birds
• Seals
• Whales and dolphins
• Dugong.