The marine dinoflagellates species belonging to the genera Dinophysis and Phalacroma have been reported as mixotrophic or heterotrophic actively feeding on planktonic ciliates. However, limited information is available on the identification of ciliate species preyed on by Phalacroma mitra. An effective method is introduced for detecting prey DNA of dinoflagellates belonging to these two genera. Three cells of P. mitra possessing food vacuoles were isolated from natural seawater, and the prey DNA within the vacuoles was analyzed. After the polymerase chain reaction (PCR)-based amplification, a restriction enzyme specific to the DNA of Dinophysis and Phalacroma was used to concentrate the prey DNA. Gene cloning revealed that the undigested PCR products contained DNA of ciliate species (Euplotes sp., Mesodinium rubrum, Spirostrombidium sp., etc.), as well as that of dinoflagellates, cryptophytes, and radiolarians. These results imply that the prey diversity of P. mitra can be traced. Furthermore, this method can provide useful data to reveal novel insights into food webs in the planktonic ecosystem. [ABSTRACT FROM AUTHOR]