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Croajingolong National Park, together with NSW's Nadgee Nature Reserve, is part of the largest coastal conservation reserve on the south eastern Australian mainland. The marine national park is adjacent to the Cape Howe wilderness area, and contains a high diversity of intertidal and shallow subtidal invertebrates. Many species from warmer northern waters reach their southern limits in far east Gippsland.

The whole region is alive with a variety of warm and cool water fish species. Purple Wrasse, Blue-Throated Wrasse and Herring Cale dart amongst the kelp. Large, disk-like sunfish are relatively frequent visitors, cruising slowly in the surface waters feeding on jellyfish.

Hundreds of humpback whales pass in the vicinity of the park on their annual migration between the tropics and Antarctic waters, sometimes followed by pods of Orca's. Little Penguins are common too and forage from the large rookery at Gabo Island.

A variety of reefs including granite and sandstone reefs add to the habitat complexity of the area. Low profile reefs within the park are covered in a dense forest of the brown seaweed Phyllospora that reaches over two metres in length. Beneath this thick, swirling canopy shelter many smaller seaweeds, Pyura ascidians, foliose red algae, coralline algae, brown algae (Zonaria), red sea-tulips, sponges, colourful sea-stars (eg. Pateriella calcar) and many large shells. Tiny brittle-stars, isopods and brightly coloured worms nestle around large sea-squirt congregations, which are quite dense in some areas.

Further off the coast, the seafloor tilts steeply down into deeper water. Sandstone reefs to a depth of about 50m, are heavily covered by a diverse array of sponges, hydroids, ascidians and soft corals. There is not enough light at these depths for the large brown seaweeds, and the low sandstone reefs are instead covered with small patches of leafy red seaweeds and a range of animals attached to the rocks. Sea-whips are common here and arch gracefully up from the seafloor.

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