The fatty acid composition of polar lipids and triacetylglycerols was determined in different morphophysiological types of symbiotic dinoflagellates isolated from the hydrocoral Millepora intricata and the scleractinian corals Pocillopora damicornis, Seriatopora caliendrum, Seriatopora hystrix, and Stylophora pistillata. The distribution of fatty acids differed fairly markedly among the investigated morphophysiological types of symbiotic dinoflagellates. The differences were found both in polar lipids, which are the structural components of the cell membranes, and storage lipids—triacetylglycerols. It is shown that fatty acids are useful chemotaxonomic markers for symbiotic dinoflagellates. It is assumed that the biochemical differences among the morphophysiological types of symbiotic dinoflagellates can reflect the genetic diversity of these types.