A novel OxyR (DR0615) with one conserved cysteine that senses hydrogen peroxide in Deinococcus radiodurans had been identified in our previous work. Comparative genomics revealed that D. radiodurans possesses another OxyR homolog, OxyR(2) (DRA0336). In this study, we constructed the deletion mutant of oxyR(2) and the double mutant of both the OxyR homologs to investigate the role of OxyR in response to oxidative stress in D. Radiodurans. Deletion of oxyR(2) resulted in an obviously increased sensitivity to hydrogen peroxide, and the double mutant for oxyR and oxyR(2) was significantly more sensitive than any of the two single mutants. The total catalase activity of the double mutant was lower than that of any of the single mutants, and reactive oxygen species (ROS) accumulated to a greater extent. DNA microarray analysis further suggested that oxyR(2) was involved in antioxidation mechanisms. Site-direct mutagenesis and complementation analysis revealed that C(228) in OxyR(2) was essential. This is the first report of the presence of two OxyR in one organism. These results suggest that D. radiodurans OxyR and OxyR(2) function together to protect the cell against oxidative stress.