The appearance of atmospheric oxygen from photosynthetic activity led to the evolution of aerobic respiration and responses to the resulting reactive oxygen species. In Rhodobacter sphaeroides, a photosynthetic α-proteobacterium, a transcriptional response to the reactive oxygen species singlet oxygen (¹O₂) is controlled by the group IV σ factor σ^E and the anti-σ factor ChrR. In this study, we integrated various large datasets to identify genes within the ¹O₂ stress response that contain σ^E-dependent promoters both within R. sphaeroides and across the bacterial phylogeny. Transcript pattern clustering and a σ^E-binding sequence model were used to predict candidate promoters that respond to ¹O₂ stress in R. sphaeroides. These candidate promoters were experimentally validated to nine R. sphaeroides σ^E-dependent promoters that control the transcription of 15 ¹O₂-activated genes. Knowledge of the R. sphaeroides response to ¹O₂ and its regulator σ^E–ChrR was combined with large-scale phylogenetic and sequence analyses to predict the existence of a core set of approximately eight conserved σ^E-dependent genes in α-proteobacteria and γ-proteobacteria. The bacteria predicted to contain this conserved response to ¹O₂ include photosynthetic species, as well as free-living and symbiotic/pathogenic nonphotosynthetic species. Our analysis also predicts that the response to ¹O₂ evolved within the time frame of the accumulation of atmospheric molecular oxygen on this planet.