Pueraria lobata is a perennial legume plant that produces a variety of isoflavones, such as puerarin, daidzin and daidzein. These are metabolized to equol via dihydrodaidzein and tetrahydrodaidzein by the bacterial fermentation of natural isoflavone sources in the human intestines. In this study, we described the growth and accumulation of isoflavone in the hairy root of the Korean wild arrowroot according to the culture period, as well as dihydrodaidzein biosynthesis in hairy root extracts fermented with Pediococcus pentosaceus. Daily proliferation was best in DY1 cultured for 1 week. DY1 showed significant differences in daily production of puerarin and daidzin+daidzein, as compared to DJ7; furthermore, both were best in DY1 cultured for 1 week. The hairy root extract was fermented successfully with P. pentosaceus with confirmed production of dihydrodaidzein, an equol precursor formed by biotransformation. The results indicated that the growth of hairy roots and isoflavone accumulation in the hairy roots is best 1 week after culture. These results are expected to contribute to the mass production of hairy root and isoflavones as equol precursors from the Korean wild arrowroot and provide a basis for equol production by biotransformation in vitro.