The aim of this study is to determine the outbreaks of nontoxic Gonyaulax polygramma Stein in Yeosu waters in place of harmful Cochlodinium polykrikoides Margalef, which has occurred annually in the same region since 1995. The observation of cellular arrangement and structure by electron microscopy showed that G. polygramma isolated from Yeosu waters had a few spines connecting with membranes and prominent longitudinal ridges on the cell surface, with a cingular displacement 1.5 times their cell width. Furthermore, the location of the nucleus was posterior of large oval formation according to electron microscopy. On 6 August, 2004, the first bloom of G. polygramma occurred, the date of its disappearance was with a maximum cell density of 8,000 cells $ml^{-1}$ on 21 August, 2004. During the period of this study, the horizontal distribution of sea water temperature and salinity showed a strong coastal front, whereas the front of DIN (Dissolved Inorganic Nitrogen) was significantly different between the occurrence and disappearance of G. polygramma blooms. These results suggested that the process of the breakdown of stratification by wind and a low level of inorganic nitrogen play important roles in the rapid growth of G. polygramma, which is associated with a greater robustness in growth against DIN than that of C. polykrikoides in nature.