In Japan, a paralytic shellfish poison (PSP) event caused by Gymnodinium catenatum Graham, a naked, colonial and PSP dinoflagellate, was first reported from Senzaki Bay, western part of the Sea of Japan in 1986. Since then, the geographical distribution of this species seems to have expanded through West Japan. To clarify the possibility of its migration being due to anthropogenic agency the historical occurrence of G. catenatum in Japanese coastal waters was examined; core sediments that preserve an historical record of this species were collected from several coastal areas where it had been observed. From the cores collected from Imari Bay, smaller spherical cysts ornamented with fine reticulated structure and with epicystal archeopyle are found which are probably different from Gymnodinium nolleri. Low cyst concentrations of G. catenatum in these cores may have resulted from such a characteristic physiological feature as chain formation of its vegetative form. The earliest occurrence of this species was recorded in sediment of Omura Bay dated to ca. 1700 A.D. This fact strongly suggests that the occurrence of G. catenatum in Japan is natural and that it has not been artificially introduced from different areas.