In this study, the possible application of Lactobacillus strains as a functional starter culture to ferment Samso-Eum (SE), an oriental herbal medicine formula, and the production of bioactive isoflavones (daidzein, genistein) were investigated. Four strains of Lactobacillus (Lactobacillus plantarum KFRI 144, L. amylophilus KFRI 161, L. curvatus KFRI 166, and L. bulgaricus KFRI 344) were used for SE fermentation. Declines in pH and in viable cell counts during fermentation were investigated and the quantification of isoflavones using HPLC were performed after fermentation at $37^{circ}C$ for 48 h. All the tested Lactobacillus strains lowered the pH level to approximately 3.6 after 48 h and showed the highest level of growth at 24 h during SE fermentation. During the SE fermentation of the four Lactobacillus strains, the conversion of isoflavone glycosides (daidzin, genistin) into bioactive aglycones (daidzein, genistein) was observed in all of the fermentations, but with different rates depending on the strains. L. plantarum KFRI 144 and L. amylophilus KFRI 161 exhibited the highest bioconversion rate of isoflavone glycosides into their bioactive aglycones. These results demonstrate that L. plantarum KFRI 144 and L. amylophilus KFRI 161 have potentials as functional starter cultures for manufacturing fermented SE with higher isoflavone bioavailability.