A self-organizing fuzzy logic controller using a genetic algorithm is described, which controlled the glucose concentration for the enhancement of flavonoid production in a fed-batch cultivation of Scutellaria baicalensis G. plant cells. The substrate feeding strategy in a fed-batch culture was to increase the flavonoid production by using the proposed kinetic model. For the two-stage culture, the substrate feeding strategy consisted of a first period with 28 g/I of glucose to promote cell growth, followed by a second period with 5 g/I of glucose to promote flavonoid production. A simple fuzzy logic controller and the self-organizing fuzzy logic controller using a genetic algorithm was constructed to control the glucose concentration in a fed-batch culture. The designed fuzzy logic controllers were applied to maintain the glucose concentration at given set-points of the two-stage culture in fed-batch cultivation. The experimental results showed that the self-organizing fuzzy logic controller improved the controller`s performance, compared with that of the simple fuzzy logic controller. The specific production yield and productivity of flavonoids in the two-stage culture were higher than those in the batch culture.