Question: Why do some corals have zooxanthellae and others do not?

Answer:  Corals are a diverse, paraphyletic group of cnidarians that are only grouped together on the basis of having some form of hard skeleton.  Only coral reef corals that need shallow, warm, clear waters for photosynthesis have zooxanthellae – only about 15% of all coral species are coral reef builders. Approximately 85% of corals are not associated with coral reef construction and live in diverse marine areas from polar seas to the tropics and from sea level to over 8000 m in depth (octocorals and hard corals are known from as deep as 6300 m, while a black coral has been recorded from 8600 m). Algal symbiosis is necessary for just a minority of coral species to be able to produce enough calcium carbonate to deposit reef-building material over time that eventually becomes biogenic limestone.