SoxR is a transcription activator governing a cellular response to superoxide and nitric oxide in Escherichia coli. SoxR protein is a homodimer, and each monomer has a redox-active [2Fe-2S] cluster. Oxidation and reduction of the [2Fe-2S] clusters can reversibly activate and inactivate SoxR transcriptional activity. Here, we use electron paramagnetic resonance (EPR) spectroscopy to follow the redox switching process of SoxR protein in vivo. SoxR [2Fe-2S] clusters are in the fully reduced state during normal aerobic growth, but are completely oxidized after only 2 minutes' aerobic exposure of cells to redox-cycling agents such as paraquat. Cellular reducing activities act rapidly on the oxidized SoxR [2Fe-2S] clusters once the oxidative stress is removed. The kinetics of SoxR [2Fe-2S] cluster oxidation and reduction exactly parallel the increase and decrease of transcription of soxS, the target gene for SoxR. Our data also indicate that an oxidative stress-linked decrease in soxS mRNA stability contributes to the rapid attainment of a new steady state after SoxR activation. Such a redox stress-related change in soxS mRNA stability may represent a new level of biological control.