Threatened and protected species include the weedy sea dragon, eastern blue devil fish, elegant wrasse, grey nurse shark and great white shark.
- Species protected in NSW include
- The weedy sea dragon is only found in southern Australian waters. It looks like a piece of seaweed and is easily camouflaged. It can be found in a variety of habitats, including shallow estuaries and deep offshore reefs. Juveniles are often associated with kelp and seagrass habitats.
- The eastern blue devil fish is brightly coloured (blue, yellow and white), very shy and found in caves, crevices and under ledges on inshore reefs and estuaries from southern Queensland to Montague Island.
- Elegant wrasse is found in similar habitats and locations as the eastern devil blue fish, and around Lord Howe Island. This subtropical, warm-temperate species is active during the day, grows to about 30 cm and the male is brightly coloured.
- North Head and Wagonga Inlet are popular locations for the threatened black rockcod.
- Montague Island and Tollgate Islands are the park's most significant and critical habitat sites for the endangered grey nurse shark.
- Great white sharks are listed as a vulnerable species in NSW and are periodically sighted in the marine park. Tagging studies show that they often pass along this coast northwards, presumably to breed.
- The marine sea mollusc Smeagol hilaris is a critically endangered species in NSW and is found in a single location on the Murramarang coast, near South Durras.
- Marine mammals, including humpback (Megaptera novaeangliae), southern right (Eubalaena australis) and killer (Orcinus orca) whales are common within the park. The park has large Australian and New Zealand fur seal populations.
- Seabirds and shorebirds, including little terns, hooded plovers, sooty and pied oyster catchers and albatross, have been recorded nesting or foraging in the Marine Park.
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