Organic-walled resting cysts of Protoperidinium parthenopes Zingone & Montresor 1988 were collected from a sediment trap in Omura Bay, western Japan. The cysts are spherical and pale brown in color. The cyst wall has two layers: a thick endophragm with granulate surface, and a thin periphragm. Three complete and incomplete parasutures appear on the surface of the endocyst. The archeopyle formed on the endocyst is basically saphopylic and compound with some combination of complete and incomplete parasutures. The cyst of Protoperidinium parthenopes closely resembles the cyst of Protoperidinium americanum (Gran & Braarud 1935) Balech 1974, but differs in the shape of the periphragm, the cyst diameter, and in the archeopyle.