Energy‐converting symbionts and organelles may be central to the cnidarian stress response. Stress may damage photochemistry in the endosymbiotic dinoflagellate Symbiodinium spp., leaving photosystems I and II relatively reduced and increasing reactive oxygen species (ROS). Alternatively, ROS may emanate from mitochondria of either the host or the symbiont, or both. These sources of ROS can be distinguished by using microscopy to examine the effects of light on stressed cnidarians incubated in the dark with a fluorescent, ROS‐detecting probe. Experiments were carried out with three species of alcyonacean octocoral, Phenganax parrini, Sarcothelia sp., and Sympodium sp. After incubation of colonies for 1 h at elevated temperature, imaging and illumination (excitation 450–490 nm, emission 515–565 nm) were begun simultaneously. Formation of ROS largely corresponded to the onset of illumination. On the other hand, chlorophyll fluorescence (excitation 530–580 nm, emission 620–690 nm) did not conform to this pattern. This difference is consistent with the expected rates of reaction. Remarkably, treatment with the inhibitor 3‐(3,4‐dichlorophenyl)‐1,1‐dimethylurea (DCMU) resulted in dramatically higher levels of light‐induced ROS. Chlorophyll fluorescence was higher in the DCMU treatment but not significantly so. By controlling for variation between individual symbionts, however, DCMU produced significantly greater levels of chlorophyll fluorescence, indicating the expected greater reduction of photosystem II. A brief exposure to light and thermal stress produced a similar effect in all three species. In addition to ROS being initiated by light, these results indicate that: (1) a brief period of stress shifts photosystem redox state toward reduction, (2) photosystem II can donate electrons to oxygen when blocked with DCMU, and (3) chlorophyll fluorescence is highly variable among individuals of Symbiodinium. Imaging of individual symbionts in hospite thus provides a powerful method for understanding the initial steps of the cnidarian stress response.