We have cultured the bluefin tuna in Yokjido, Tongyeong with floating cage which was vulnerable to harmful dinoflagellate, Cochiodinium polykrikoides. This study inspected a vertical migration of phytoplankton and Chl-a for reasonable sinking depth in floating cage. Furthermore, we analyzed the fluctuation of the phytoplankton including harmful dinoflagellates occurring in Yokgido for 6 years. Total cell density showed a significant monthly variation and the flora was predominated with diatoms. Gymnodinium sp. occurred 19 times, the greatest number of occurrence in all kinds of dinoflagellates during summer. In particular, the total number of occurrence at C. polykrikoides was 8, and harmful dinoflagellates such as Karenia brevis/Fibrcapsa japonica occurred. The relationship between Chl-a concentration/total cell number and sunset/sunrise was significant and reasonable sinking depth in floating cage was found to be at least 3m from the water surface, which was associated with massive fish kills caused by C. polykrikoides.