The temperature-induced collapse ("bleaching") of the coral-dinoflagellate symbiosis is hypothesised to result from symbiont oxidative stress and a subsequent host innate immune-like response. This includes the production of nitric oxide (NO), which is involved in numerous microbial symbioses. Much of NO's cytotoxicity has been attributed to its conversion, in the presence of superoxide (O2-), to highly reactive peroxynitrite (ONOO-). However, ONOO- generation has yet to be observed in either a lower invertebrate or intracellular mutualism. Using confocal laser scanning microscopy with the fluorescent ONOO- indicator aminophenyl fluorescein (APF), we observed strong evidence that ONOO- is generated in symbiotic Aiptasia pulchella under conditions known to induce thermal bleaching. However, a role for ONOO- in bleaching remains unclear as treatment with a peroxynitrite scavenger had no significant effect on thermal bleaching. Therefore, while ONOO- may have a potential for cytotoxicity, in vivo levels of the compound may be insufficient to affect bleaching.