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In this study, we compared the spatio-temporal differences of phytoplankton communities among 4 lakes in the Boseong River basin. Field research was conducted quarterly from 2014 to 2017 for this study. A total of 345 species of phytoplankton were identified including 107 Bacillariophyceae, 175 Chlorophyceae, 27 Cyanophyceae and 36 other phytoplankton taxa. Lake Boseong showed higher species numbers and density of phytoplankton than other lakes (Dunn’s test, P<0.01). Bacillariophyceae such as Asterionella formosa, Aulacoseira granulata, Fragilaria crotonensis was dominated in most research periods, whereas Scenedesmus ecornis and Coelastrum cambricum belonging to Chlorophyceae were dominant species on August. The self-organizing map (SOM) classified 3 clusters with 10×7 grid and showed spatio-temporal variation of phytoplankton communities based on significant difference among each clusters. Total 31 species of phytoplankton were chosen as a indicator species using indicator species analysis (ISA) and reflected seasonal phytoplankton succession and diversity and density of phytoplankton according to nutrient concentration. Water temperature, Secchi depth, conductivity and DO were identified as important factors affecting the differences of phytoplankton communities in the studied lakes in Boseong River basin using non-metric multidimensional scaling (NMDS).