Marine microalgae produce various types of compounds, including nitrogenous neurotoxins, polyether sea food toxins, sulfonium compounds of dimethyl sulfide precursors and antineoplastic macrolides. Among them, dinoflagellate metabolites such as ciguatoxin and maitotoxin are unique and spectacular in terms of their complex structures, potent activities and intricate biogenesis. Symbiotic dinoflagellates so-called zooxanthellae are distributed over a wide range of marine invertebrates and were thought to produce bioactive metabolites which were isolated from marine invertebrates containing zooxanthella inside of the body. However, most trials failed to establish the production of bioactive substances by symbiotic organisms because of difficulties of their culture and adjustment of the culture conditions for the desired metabolite production. In studies on the biogenesis of vasocontrictive macrolides, zooxanthellatoxins isolated from a symbiotic dinoflagellate Symbiodinium sp., we have investigated metabolites of the dinoflagellate cultured under different conditions. Four new compounds were isolated from 70% EtOH extract of the cells cultured in an f/2 medium. Two betaines (zooxanthellabetaine-A and -B) were obtained from a neutral fraction of n-BuOH soluble portion and the structure of zooxanthellabetaine-A was determined as 4-(4-hydroxybenzoyloxy)-3-(trimethylammonio)-butyrate. The EtOAc soluble portion afforded a new C-30 alkaloid, zooxanthellamine, and a new ceramide, symbioramide-C16. The structural similarity of zooxanthellamine to zoanthid alkaloids, zoanthamines, suggested an algal origin of these zoanthamines. Zooxanthellamine might be derived biogenetically from a polyketide chain presumably started from a glycine unit, like other marine toxins such as zooxanthellatoxin and palytoxin.