The ability of phototrophs to convert light into biological energy is critical for life on Earth. However, there can be deleterious consequences associated with this bioenergetic conversion, including the production of toxic byproducts. For example, singlet oxygen ( ¹ O ₂ ) can be formed during photosynthesis by energy transfer from excited triplet-state chlorophyll pigments to O ₂ . By monitoring gene expression and growth in the presence of ¹ O ₂ , we show that the phototrophic bacterium Rhodobacter sphaeroides mounts a transcriptional response to this reactive oxygen species (ROS) that requires the alternative σ factor, σ ^E . An increase in σ ^E activity is seen when cells are exposed to ¹ O ₂ generated either by photochemistry within the photosynthetic apparatus or the photosensitizer, methylene blue. Wavelengths of light responsible for the generating triplet-state chlorophyll pigments in the photosynthetic apparatus are sufficient for a sustained increase in σ ^E activity. Continued exposure to ¹ O ₂ is required to maintain this transcriptional response, and other ROS do not cause a similar increase in σ ^E -dependent gene expression. When a σ ^E mutant produces low levels of carotenoids, ¹ O ₂ is bacteriocidal, suggesting that this response is essential for protecting cells from this ROS. In addition, global gene expression analysis identified ≈180 genes (≈60 operons) whose RNA levels increase ≥3-fold in cells with increased σ ^E activity. Gene products encoded by four newly identified σ ^E -dependent operons are predicted to be involved in stress response, protecting cells from ¹ O ₂ damage, or the conservation of energy.