Some of the best known and best developed reefs of the mainland are those of the Hengchun Peninsula and the Kenting National Park. These are fringing communities, although they form a discontinuous structure broken up by sand channels. These reefs are further characterized by significant variation in the fauna between localities, with certain areas dominated by alcyonarian coral. Some 250 scleractinian corals from 58 genera have been recorded, together with 39 species (11 genera) of alcyonarian coral. Fringing reefs are also well developed around the offshore islands. In the northern parts of the South China Sea there are diverse fringing reefs around Hsiao-Liu-Chiu, while further north there are patchy coral reefs and occasional fringing reefs around the Pen-Hu (Pescadores) Islands. The islands off the east coast include Lan-Yu and Lu-Tao, both of which are volcanic. These lie in the path of the Kuroshio Current and diverse reef communities have developed. In 1998 there was extensive coral bleaching, and surveys in 1999 and 2000 have suggested that about 20 percent of coral colonies died during this event.

There are extensive fringing reefs and some platform reefs around the main island and some of the smaller islands. The species diversity is relatively high, with about 300 hard coral species, 70 soft coral and gorgonian species, and 1200 fish species. The reefs are under the impact of typhoons and have not been invaded by the crown-of-thorns starfish.

Coral reefs occur in all waters around Taiwan except on the sandy west coast areas. The best-developed fringing reefs are around the southern tip of the island - the Hengchun Peninsula. These reefs have diverse and abundant hard and soft corals. There are patchy coral communities elsewhere around the island, with a dominance of hard corals. Rich coral reefs occur around the offshore islands of Lutao (Green Island), Lanyu (Orchid Island) off southeast Taiwan, Hsiaoliuchiu and Penghu Islands (the Pescadores) to the southwest, and the Penghu Archipelago 50 km west off Taiwan in the Taiwan Strait.

True and well-developed reef systems are found in the South China Sea. There are about 128 atolls in the South China Sea, including the islands of Dongsha, Xisha, Zhongsha and Nansha, of which about half are emerged atolls, and another half are drowned atolls. Dongsha (Pratas) Island and Taiping (Itu Aba) Island in the South China Sea are flourishing atolls. However, coral cover on Dongsha Island has declined, following intensive overfishing and coral bleaching, to less than 10%.