Daidzin, daidzein 7-O-glucoside, is a major isoflavone in soybean and acts as a phytoestrogen. By intestinal bacteria dietary, daidzin is hydrolyzed to the aglycone daidzein and further converted to the more reduced metabolites, such as dihydrodaidzein, tetrahydrodaidzein, and equol. Human intestinal bacteria Enterococcus sp. MRG-2 and Lactococcus sp. MRG-IF-4, which convert daidzin to daidzein, were isolated under anaerobic condition, and identified by 16S rRNA gene sequence analysis. Changes of OD 600 and pH were measured during the anaerobic growth, and deglycosylation kinetics of daidzin and genistin were measured by HPLC. Both bacteria also converted other isoflavone 7-O-glucosides, glycitin, ononin, and sissotrin, to their aglycones, glycitein, formononetin, and biochanin A, respectively. Apigetrin was deglycosylated to apigenin by these bacteria too. However, rutin, hesperidin, and naringin were not converted to the aglycones. Phylogeny analysis of the isolated strains also found that bacterial species identified by 16S rRNA gene sequence was not correlated with its metabolic ability of flavonoid biotransformation.