Zooxanthellae are golden-brown endosymbionts of various marine animals and protozoa. They are typically dinoflagellate algae, although other algae such as diatoms can also be zooxanthellae . They are often acquired by direct ingestion, and subsequently multiply in the host's tissues, providing it with various nutrients. Their population in the host tissue is limited by controlling the amount of food and light they receive and by digestion of excess cells.

Hermatypic (reef-building) corals have zooxanthellae and are largely dependent on them, limiting their growth to the photic zone. The symbiotic relationship is probably responsible for the phenomenal success of corals as reef-building organisms in tropical waters.

Other organisms which may have zooxanthellae include jellyfish, clams, sea slugs, and radiolaria. There are several different species of zooxanthellae, typically grouped together as the genus Symbiodinium, which appears to be monophyletic.