An animal lignin, enterodiol (END), is known to be formed by conversion of secoisolariciresinol from flaxseed by intestinal bacteria. Thirteen bacteria strains were examined for their hydroxylation activity for END. Among them, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152 showed the highest hydroxylation activity for END. Reaction products profiled using GC/MS revealed that four products mono-hydroxylated in aliphatic position (Al-OH-END) and three products mono-hydroxylated in aromatic ring (Ar-OH-END) were found in S. avermitilis MA-4680, whereas only two Ar-OH-ENDs were detected in the case of N. farcinica IFM10152. From 15mg/L of END, 900 μg/L of Al-OH-END and 210 μg/L of 4-hydroxy END (4-OH-END) were produced by S. avermitilis MA-4680, and 300 μg/L of 2-hydroxy END (2-OH-END) and 480 μg/L of 4-OH-END were obtained by N. farcinica IFM10152. To find the P450s are responsible for the substrate specificity to END, 33 P450s from S. avermitilis MA-4680 and 26 P450s from N. farcinica IFM10152 were cloned and compared with coexpression of putidaredoxin reductase (camA) and putidaredoxin (camB) from Pseudomonas putida as redox partners in E. coli. As a result, Nfa45180 showed the highest hydroxylation activity especially for ortho-hydroxylation in aromatic ring in vivo. The results of the docking simulation of END into the homology model of Nfa45180 explained the reason for regio-specificity of the hydroxylation. To our knowledge, this is the first report of regioselective hydroxylation of END using microorganism P450s.