Puerarin and daidzein are the major naturally occurring isoflavones in leguminous plants. These two compounds are metabolized to equol by human intestinal flora. Here we isolated two intestinal bacteria capable of metabolizing puerarin and daidzein, respectively, from human feces. One of them, strain PUE, converted puerarin to daidzein by cleaving a C-glucosyl bond, whereas the other, strain DZE, converted daidzein to equol by reducing a double bond in ring C followed by elimination of an oxo group. Based on the 16S ribosomal RNA gene sequence, strain DZE showed 85% similarity with Eggerthella lenta. Equol produced by strain DZE was identified as (3S)-equol through several analytical methods. Moreover, we obtained (3S)-equol from puerarin by co-incubation with strain PUE and DZE. In addition, 5-hydroxyequol was obtained from genistein by incubation with strain DZE.