Aims Secoisolariciresinol (SECO) is increasingly recognized for potential clinical application because of its preventive effects against breast and colon cancers, atherosclerosis and diabetes, and its production through biotransformation has been attempted. However, previously reported bacteria all required stringent anaerobic culture conditions, precluding large‐scale production. Here, we report the isolation and characterization of bacteria that produce SECO under less stringent anaerobic culture conditions. Methods and Results Using defatted flaxseed as raw material, we isolated a facultative anaerobic bacterium from human faeces that hydrolysed secoisolariciresinol diglucoside‐3‐hydroxy‐3‐methyl glutaric acid (SDG‐HMGA) oligomers in flaxseed to produce SECO. Both conventional assays and 16S rRNA gene sequence analysis demonstrated its close relatedness with Bacteroides uniformis. The transformation efficiency of SDG in defatted flaxseed to SECO was more than 80% by this bacterial strain. We investigated factors that might influence fermentation, such as redox potential and pH, for large‐scale fermentation of defatted flaxseed to produce SECO. Conclusions The method to produce SECO through biotransformation of defatted flaxseed with this bacterial strain is highly efficient and economic. Significance and Impact of the Study This bacterial strain can transform SDG to SECO under less stringent anaerobic culture conditions, which will greatly facilitate industry‐scale production of SECO.