Zooxanthellae are unicellular, golden-brown algae (dinoflagellates) that live either in the water column as plankton or symbiotically inside the tissue of other organisms. The most common symbiotic association is with hard, reef-building (or hermatypic) corals, although zooxanthellae can also be found living inside the tissue of soft corals, jellyfish, giant clams and nudibranchs.

Zooxanthellae live symbiotically in the surface tissues of coral polyps through a tight recycling of waste and food products. Corals provide the zooxanthellae with a constant, protected environment and an abundance of nutrients (carbon dioxide, nitrogenous and phosphorus wastes from the cellular respiration of the coral's tissues). In return, the coral receives a constant supply of oxygen and other photosynthetic products (carbohydrates) from the zooxanthellae.

The organic material produced by the zooxanthellae through photosynthesis is transferred to the coral host, satisfying up to 90% of the coral's nutrient and energy requirements. The remainder is satisfied through active feeding on external food sources, particularly plankton.

Because the photosynthetic products produced by the zooxanthellae are an essential component of the coral's diet, hard, reef-building corals are generally limited to shallow waters (< 50 m) where they receive sufficient sunlight for photosynthesis. Water clarity also has a considerable influence on the depths at which corals can live because it directly affects light penetration. In areas where there are large amounts of suspended sediment such as near the mouths of estuaries or where there has been terrestrial run-off from coastal developments, light penetration can be severely reduced, limiting the distribution of coral to the upper few metres.

When subjected to environmental stresses such as high or low temperatures, low salinity, high light intensity or pollutants, zooxanthellae may be expelled or digested by the coral host causing coral bleaching. If the environmental stress is short-lived, corals can recover by regaining zooxanthellae from the surrounding water or by multiplication of those that remain. If unfavourable conditions are prolonged, corals may remain bleached and will eventually die.

Initially, it was thought that there was only one species of zooxanthellae (Symbiodinium microadriticum). However, with the advent of electron microscopy and molecular tools, it has since been discovered that zooxanthellae consitutue a variety of taxa. Most still belong to the genus Symbiodinium, but to different 'clades'. To date, five distinct clades (A, B, C, D and E) have been identified. Each of these clades has varying thermal tolerances and capacities to deliver photosynthetic products to their coral host. On the GBR, zooxanthellae belonging to clade C are most common, However, clade C zooxanthellae are less heat tolerant than those belonging to clade D, which tend to be found in corals living in northern and inshore sections of the GBR. It is thought that corals expel symbionts that are intolerant to the prevailing conditions, on the chance that they may be able to acquire more tolerant zooxanthellae from the surrounding water. The variation in thermal tolerances of different zooxanthellae clades and the ability of the coral hosts and their zooxanthellae symbionts to adapt to changing sea temperatures will be important factors determining the long-term resilience of the GBR to climate change.