In order to evaluate the application of Algae Online Analyzer (AOA), an instrument of automatic measurement of chlorophyll a concentration, was tested and compared with the acetone extraction method on the basis of microscopic counting of phytoplankton in field water (Paltang Reservoir). We simultaneously conducted AOA operation and extraction method with the same water sample, to compare both results of chlorophyll a measurement. Phytoplankton were enumerated by inverted microscope with the Sedgwick-Rafter chamber, and classified into the genus or species. According to the AOA measurement, the diatom most (83.6%) strongly contributed to the total chlorophyll a concentration, followed by chlorophyceae> cyanophyceae>cryptophyceae. Overall, the results of both AOA and extraction method showed a similar trend and significant correlation (r=0.87, n=302, p<0.001), however, there were some differences according to the season and species. In particular, the relationship between AOA Chl-a density of the diatom (r=0.73, p=0.010) and cyrptophyceae (.=0.83, p=0.00154) were siginificant, while chlorophyceae (r= -0.13) and cyanophyceae (r= -0.16) showed no clear relationship during the study period. Although we can not fully understand why there was difference between both mothods, AOA application for alarming algal bloom and water quality management during the algal bloom appears to be very relevant. However, the further study or technical upgrade of AOA measurement is required, especially in the case of low density of phytoplankton or species-specific measurement.