[Objective] Compared to the original bacterium strain AUH-JLC140, its oxygen-tolerant mutant strain named Aeroto-AUH-JLC140 was able to produce an unknown substance. In addition, the production of the unknown substance was not associated with the addition of the substrate daidzein to the cultural medium. The objective of this study was to isolate and identify the unknown substance, and then to study the kinetics and the anti-oxidative capacity of the unknown substance produced by the oxygen-tolerant mutant strain Aeroto-AUH-JLC140. [Methods] The unknown substance was isolated by high-performance liquid chromatography (HPLC) method. Based on the analyses of the UV spectrum, electrospray ionization mass spectrometry (ESI-MS) as well as the 1H and 13C nuclear magnetic resonance spectroscopy, the unknown substance was identified. The anti-oxidative activity of the unknown substance was determined by the 1,1-Diphenyl-2-Picrylhydrazyl (DPPH) scavenging activity. [Results] The unknown substance produced by the oxygen-tolerant mutant strain Aeroto-AUH-JLC140 was identified as indole. Kinetics study showed that indole reached to the highest after being incubated for 15 h and the highest amount of indole in the cultural broth was 19.89 mg/L. Study on free radical-scavenging activity indicated that 0.2 mmol/L (i.e. 23.40 mg/L) of indole not only showed an obvious DPPH radical-scavenging activity but also decreased the oxidation-reduction potential (ORP) of brain heart infusion (BHI) liquid medium. [Conclusion] The unknown metabolite produced by the oxygen-tolerant mutant strain Aeroto-AUH-JLC140 is indole. The amount of indole produced by strain Aeroto-AUH-JLC140 can decrease the ORP of BHI liquid medium, which subsequently provides a suitable microenvironment with lower ORP for growth of strain Aeroto-AUH-JLC140 in the presence of atmospheric oxygen.