Zooxanthellae are single-celled dinoflagellates that live in symbiosis with diverse marine invertebrates including demosponges, corals, jellyfish, and nudibranchs. They are autotrophs containing chloroplasts composed of thylakoids present in clusters of three. A pyrenoid protrudes from each chloroplast and is encased along with the chloroplast by a thick, starchy covering. Within the cell’s cytoplasm also exists lipid vacuoles, calcium oxalate crystals, dictyosomes, and mitochondria. The cell wall of zooxanthellae varies in structure across species.

Zooxanthellae are particularly associated with reef-building corals but they also inhabit other invertebrates and protists. They help the coral survive by providing it with food resulting from photosynthesis. In return, the zooxanthellae produce oxygen and help the coral to remove wastes. Most importantly, zooxanthellae supply the coral with glucose, glycerol, and amino acids, which are the products of photosynthesis. The coral uses these products to make proteins, fats, and carbohydrates, and produce calcium carbonate.

Zooxanthellae are responsible for the unique and beautiful colors of many stony corals. Sometimes when corals become physically stressed, the polyps expel their zooxanthellae and the colony takes on a stark white appearance. This is commonly described as “coral bleaching”. If the polyps go for too long without zooxanthellae, coral bleaching can result in the corals death.