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The presence of zooxanthellae is so important to the health of the coral that scientists speculate the symbiotic algae must have been present in the polyp tissue almost throughout modern coral's 50-100 million years of evolution.

The zooxanthellae alga has been dubbed Symbiodinium microadriaticum, part of a "supergenus" of marine dino-flagellate algas, but recent research suggests there are more than one species. These algas are dinoflagellates, which have whip-like processes giving them some limited ability to move. This is probably how the cells initially enter the corals, although once they are there they divide vegetatively, and take on a simpler structural form.

Corals are not the only reef animals to have zooxanthellae. Sea anemones and other cnidarians host the algae, as do some molluscs, most famously the giant clams (Tridacna). Because zooxanthellae is a yellow-brown algae, and the host tissues are generally colorless—to pass the greatest amount of light to the algae—zooxanthellae-containing animals are usually a dull color: beige, brown, olive green. There are exceptions, however, including some of the giant anemones and Tridacna clams, which can be richly hued. As a general rule, however, the most brightly colored invertebrates—such as some of the soft corals—do not harbor zooxanthellae.