A continuous imaging system equipped with fluorescent imaging for counting, measuring size of individual cell and classification of phytoplankton has been developed. Fluorescent imaging is very useful to distinguish phytoplankton from other particles. Our system allows us to count cell numbers and measure individual cell size as accurate as microscopy measurement. Moreover, the measurements can be carried out at high speed and in small sample volume. If this system is deployed in oceanographic investigations, phytoplankton distributions with high temporal and spatial resolution will be extracted. Therefore, it will contribute to studies of not only phytoplankton but also carbon cycle