In this study, we analyzed the relationship between phytoplankton community and physicochemical factors in 12 lakes located in Jeollanam-do based on the data surveyed from March to November 2014. Totally, 297 species of phytoplankton were identified including 98 Bacillariophyceae, 148 Chlorophyceae, 23 Cyanophyceae and 28 other phytoplankton taxa. The standing crops ranged from 124 to 59,148 cells mL-1 and showed the highest in August with the increase of Cyanophycean cells. The self-organizing map (SOM) was optimized into 9×6 grid and was classified into 5 clusters based on the similarity of environmental factors and phytoplankton indices. The SOM results showed that phytoplankton communities had positive relationship with water temperature, SS, DO, BOD, TP and Chl-a, whereas low relationship with pH, TN, NH3-N, NO3-N, PO4-P and Conductivity. In Pearson’s correlation coefficient, relationship between environmental factors and phytoplankton communities showed similar results with SOM.