An important environment that is more or less totally restricted to the intertropical zone is the coral reef. Coral reefs are found where the ocean water temperature is not less than 21 °C, where there is a firm substratum, and where the seawater is not rendered too dark by excessive amounts of river-borne sediment. They will not grow in very deep water, so a platform within 30 to 40 meters of the surface is a necessary prerequisite for their development. Their physical structure is dominated by the skeletons of corals, which are carnivorous animals living off zooplankton. However, in addition to corals there are enormous quantities of algae, some calcareous, which help to build the reefs. The size of reefs is variable. Some atolls are very large—Kwajelein in the Marshall Islands of the South Pacific is 120 kilometers long and as much as 24 kilometers across-but most are very much smaller, and rise only a few meters above the water. The 2,000 kilometer complex of reefs known as the Great Barrier Reef, which forms a gigantic natural breakwater off the northeast coast of Australia, is by far the greatest coral structure on Earth.

Coral reefs have fascinated scientists for almost 200 years, and some of the most pertinent observations of them were made in the 1830s by Charles Darwin on the voyage of the Beagle. He recognized that there were three major kinds: fringing reefs, barrier reefs, and atolls; and he saw that they were related to each other in a logical and gradational sequence. A fringing reef is one that lies close to the shore of some continent or island. Its surface forms an uneven and rather rough platform around the coast, about the level of low water, and its outer edge slopes downwards into the sea. Between the fringing reef and the land there is sometimes a small channel or lagoon. When the lagoon is wide and deep and the reef lies at some distance from the shore and rises from deep water it is called a barrier reef. An atoll is a reef in the form of a ring or horseshoe with a lagoon in the center.

Darwin’s theory was that the succession from one coral reef type to another could be achieved by the upward growth of coral from a sinking platform, and that there would be a progression from a fringing reef, through the barrier reef stage until, with the disappearance through subsidence (sinking) of the central island, only a reef-enclosed lagoon or atoll would survive. A long time after Darwin put forward this theory, some deep boreholes were drilled in the Pacific atolls in the 1950s. The drill holes passed through more than a thousand meters of coral before reaching the rock substratum of the ocean floor, and indicated that the coral had been growing upward for tens of millions of years as Earth's crust subsided at a rate of between 15 and 51 meters per million years. Darwin s theory was therefore proved basically correct. There are some submarine islands called guyots and seamounts, in which subsidence associated with sea-floor spreading has been too speedy for coral growth to keep up.

Like mangrove swamps, coral reefs are extremely important habitats. Their diversity of coral genera is greatest in the warm waters of the Indian Ocean and the western Pacific. Indeed, they have been called the marine version of the tropical rain forest, rivaling their terrestrial counterparts in both richness of species and biological productivity.They also have significance because they provide coastal protection, opportunities for recreation, and are potential sources of substances like medicinal drugs. At present they are coming under a variety of threats, of which two of the most important are dredging and the effects of increased siltation brought about by accelerated erosion from neighboring land areas.

珊瑚礁生长的重要环境差不多仅限于热带区域。它们一般见于海洋中的水温不低于21°C、基石坚定，并在海水没有因为过量的河流沉积物而显得太暗的环境中。它们不会生长在深水之中，所以在海平面之下30米到40米之间要有一个平台，这是珊瑚礁生长的一个必要的前提条件。珊瑚礁的物理结构主要是珊瑚的骨骼，也就是以浮游动物为食的肉食动物的尸骨。然而，除了珊瑚以外，还有大量的藻类、一些钙质都对珊瑚礁的形成有帮助。珊瑚礁的大小是不定的。一些环礁体积非常之大——南太平洋马绍尔群岛的夸贾林环礁有120千米长，24千米宽，但大多数珊瑚礁都是非常小的，只能生长到水面以上几米。被称为“大堡礁”的珊瑚礁群，长达2000千米，在澳大利亚东北海岸形成了一个巨大的天然防波堤，是地球上迄今为止最大的珊瑚结构。

科学家研究珊瑚礁已经有近200年的时间，其中1830年查尔斯•达尔文在乘坐贝格尔航行时对珊瑚礁的观察最为深入中肯。他识别出了三种主要的珊瑚礁：岸礁、堡礁和环礁；并且观察到珊瑚之间的排列是渐次有序、相互关联的。岸礁生长于靠近大陆或岛屿的岸边，它的表面粗糙不平，沿着海岸在浅水区生长，外缘向海里倾斜。岸礁和陆地之间有时会有一个小通道或泻湖。如果泻湖宽而且深，且礁生长在离岸边一段距离的深水中，这种珊瑚礁就叫堡礁。环礁是一个环形或马蹄形礁，泻湖在礁的中间。

达尔文的理论是：一种珊瑚礁类型可以演替为另一种类型，首先珊瑚会从一个正在下沉的平面上向上生长，岸礁就演变到堡礁阶段，堡礁阶段由于中央岛全部沉入海里，只剩下珊瑚环绕的泻湖或环礁留存下来。在二十世纪50年代，达尔文提出这一理论很久之后，人们在太平洋的环礁上钻了一些深孔。钻孔深达一千米，穿过珊瑚直到海底的岩石层，说明这些珊瑚已经生长了有数千万年了，因为地壳是以每一百万年15到51米的速度在下沉。因此这说明达尔文的理论基本上是正确的。有一些海底岛屿称为平顶山或海底山，在这些地方海底扩张带来的下沉速度太快，以至于珊瑚礁的生长速度跟不上。

像红树林沼泽一样，珊瑚礁是非常重要的栖息地。在印度洋和西太平洋的温暖水域中，珊瑚属的生物多样性是最大的。事实上，它们被称为海洋版的热带雨林，在物种丰富度和生物生产力方面可以与真正的热带雨林媲美。它们的重要性还体现在海岸防护、旅游娱乐和潜在的药用成分方面。目前，珊瑚礁遭受着很多的威胁，其中最重要的两种威胁是疏浚和邻近土地面积的加速侵蚀所造成的淤积增加。