Coral reefs are habitats to hundreds and thousands of organisms and are thus well known as “the rainforests in the ocean”. They constitute one of the world’s most spectacular ecosystems. Many biologists and ecologists have employed a multitude of experimental approaches in the study of coral reefs. These studies have revealed that reef systems host invaluable biodiversity. Albeit about a third of all marine organisms thrive in coral reef ecosystems, surprisingly, their total area makes up <1% of marine surface area. Furthermore, only about 10% of all species on reefs have been studied and described with the direct implication that about 90% of the species on the world’s coral reefs have remained undiscovered. There are two major coral faunas: Indo-pacific and Atlantic. The Indo-pacific reef system is characterized by relatively higher biodiversity than the Atlantic probably due to different dynamic processes taking place in these two systems. Corals are sensitive to factors such as salinity, sediment and nutrient inputs to marine systems, leading to the emergence of new and distinctive patterns. In addition to species diversity, genetic and ecological diversity has emerged as the new focus in this field. From a human perspective, coral reefs are not only a source of wonder, but also an invaluable source of marine food, medicine and industrial material. They also provide a protective role for mangrove and other near-shore ecosystems from tropical storms in addition to being an ideal treasured study destination for scientists. Different species may compliment the functions of each other in coral reef ecosystem. Recently due to anthropogenic activities and especially climate change (global warming), which have aggravated destruction on coral reef systems, biodiversity reduction and ecological function degradation have received incredible attention from researchers and nature conservationists. Therefore, the study of reef ecological function in relation to dwindling biodiversity is a current situation that requires extremely urgent attention to redress. In China, coral reef is very pretty and characterized by high biodiversity and important ecological functions, hence, the need for deep research aimed at conserving this rich ecosystem. The primary approach towards this important goal of conservation is to identify the species distribution and their ecological functions, classify and catalogue them and develop a long-term monitoring program for the coral reef dynamic processes. This approach, if effectively applied and implemented, will boost the recovery and conservation of coral reef systems not only in the South China Sea but also in other world marine environments.