In the bioluminescent dinoflagellateGonyaulax polyedra, the formation of asexual cysts was elicited either by addition of 5-methoxytryptamine or by transfer to short-day conditions under lower temperature and decreased light intensity. The resulting changes were followed in vivo by light microscopy, and analysed ultrastructurally by electron microscopy. Irrespective of the method of cyst induction, theca and flagella shedding and the formation of a cyst wall can always be observed as essential steps in this process. Despite the extremely low level of bioluminescence emitted from the cysts, some scintillons persist. Encystment is accompanied by organelle and substructure rearrangement. Although cysts induced by 5-methoxytryptamine or by short days closely resemble each other, electron microscopy reveals typical differences. In cysts obtained by treatment with 5-methoxytryptamine most chloroplasts are of the expanded type, extending to the central region, whereas only a few are compact and peripherally positioned. Cysts induced by shortdays predominantly contain chloroplasts of the compact type and contain large amounts of stored starch and lipids. Their ultrastructural organization therefore resembles that of mastigote cells during darkness.