Abstract: Many immobile freshwater dinoflagellates, including the epineustonic genus Cystodinium Klebs, belong to the order Phytodinales.Due to limited cultivation and materials, knowledge on the taxonomy, phylogenetic position and life cycle of the genus Cystodinium is limited.An algal bloom was observed in a fish pond in Wuhan, Hubei Province, China in the summer of 2013.Cells were isolated from enriched samples using a micropipette.The clonal culture (FACHB-1781) was established and maintained in the Freshwater Algae Culture Collection at the Institute of Hydrobiology, Chinese Academy of Sciences.The species was identified as Cystodinium bataviense Klebs by morphological and molecular evidence.The vegetative cells were lunate or shaped like an elongated oval with blunt horns.The poles were bluntly prolonged and without spines or projections.Phylogenetic results based on SSU rDNA sequences indicated that the order Phytodinales was not monophyletic.Some Phytodinales groups (e.g.Hemidinium nasutum and Gloeodinium viscum) did not show any consistent affiliation with any other lineage.While C.bataviense clustered with C.phaseolus, the phylogenetic position of the Cystodinium clade was still unknown.Future work on this genus will help clarify its phylogenetic position within the dinoflagellates.