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A shoal of rock, coral or other sufficiently coherent material, lying beneath the surface of water

A reef is a ridge or shoal of rock, coral, or similar relatively stable material lying beneath the surface of a natural body of water. Conversely, mounds lack a macroscopic skeletal framework. Instead, they are built by microorganisms or by organisms that also lack a skeletal framework. A microbial mound might be built exclusively or primarily by cyanobacteria. Examples of biostromes formed by cyanobacteria occur in the Great Salt Lake in Utah, United States, and in Shark Bay on the coast of Western Australia. Cyanobacteria do not have skeletons, and individual organisms are microscopic. However, they can encourage the precipitation or accumulation of calcium carbonate to produce distinct sediment bodies in composition that have relief on the seafloor. Cyanobacterial mounds were most abundant before the evolution of shelly macroscopic organisms, but they still exist today. Stromatolites, for instance, are microbial mounds with a laminated internal structure. Whereas, bryozoans and crinoids, common contributors to marine sediments during the Mississippian period, produce a different kind of mound. Although bryozoans are small and crinoid skeletons disintegrate, bryozoan and crinoid meadows can persist over time and produce compositionally distinct bodies of sediment with depositional relief. The Proterozoic Belt Supergroup contains evidence of possible microbial mat and dome structures similar to stromatolite and chicken reef complexes.

Rocky reefs are underwater outcrops of rock projecting above the adjacent unconsolidated surface with varying relief. They can be found in depth ranges from intertidal to deep water, and provide a substrate for a large range of sessile benthic organisms, and shelter for a large range of mobile organisms. Corals, including some major extinct groups Rugosa and Tabulata, have been important reef builders through much of the Phanerozoic since the Ordovician Period. However, other organism groups, such as calcifying algae, especially members of the red algae (Rhodophyta), and molluscs (especially the rudist bivalves during the Cretaceous Period) have created massive structures at various times. During the Cambrian Period, the conical or tubular skeletons of Archaeocyatha, an extinct group of uncertain affinities (possibly sponges), built reefs. Other groups, such as the Bryozoa, have been important interstitial organisms, living between the framework builders. The corals which build reefs today, the Scleractinia, arose after the Permian–Triassic extinction event that wiped out the earlier rugose corals (as well as many other groups). They became increasingly important reef builders throughout the Mesozoic Era. They may have arisen from a rugose coral ancestor. Rugose corals built their skeletons of calcite and have a different symmetry from that of the scleractinian corals, whose skeletons are aragonite. However, there are some unusual examples of well preserved aragonitic rugose corals in the Late Permian. In addition, calcite has been reported in the initial post larval calcification in a few scleractinian corals. Nevertheless, scleractinian corals (which arose in the middle Triassic) may have arisen from a non calcifying ancestor independent of the rugosan corals (which disappeared in the late Permian).