Zooxanthellae are unicellular yellow-brown (dinoflagellate) algae which live symbiotically in the gastrodermis of reef-building corals (Goreau et al., 1979). It is the nutrients supplied by the zooxanthellae that make it possible for the corals to grow and reproduce quickly enough to create reefs. Zooxanthellae provide the corals with food in the form of photosynthetic products. In turn, the coral provides protection and access to light for the zooxanthellae.

Because of the need for light, corals containing zooxanthellae only live in ocean waters less than 100 meters deep (Goreau et al., 1979). They also only live in waters above 20 degrees Celsius and are intolerant of low salinity and high turbidity (Goreau et al., 1979).

It was once believed that all zooxanthellae were the same species, Symbiodinium microadriaticum (Rowan and Powers, 1991). However, recently, zooxanthellae of various corals have been found to belong to at least 10 different algal taxa. Interestingly, zooxanthellae found in closely related coral species are not necessarily closely related themselves, and zooxanthellae found in distantly related coral species may, in fact, be closely related (Rowan and Powers, 1991). This suggests that coral and zooxanthellae evolution did not occur in permanently associated lineages. Rather, symbiotic recombination probably shaped the evolutionary process, allowing both symbionts to evolve separately.