The fluorescent protein KillerRed generates reactive oxygen species through the CALI effect. This property paves the way for the design of genetically encoded photosensitizers for use in cell killing and cancer photodynamic therapy. In this article, we have investigated the diffusion pathways of di-oxygen and the superoxide radical in KillerRed, using molecular dynamics simulations. Our results suggest that, by comparison to the Ser-65-Thr mutant of GFP, diffusion of molecular oxygen (and singlet oxygen) is greatly facilitated in KillerRed, mostly due to the presence of a unique water-filled channel. In contrast, due to their negative charge, superoxide radical ions putatively produced inside the chromophore pocket are unable to escape the protein. These results are consistent with the hypothesis that superoxide generation, if it occurs, proceeds via light-induced photoreduction of the chromophore followed by long-range electron transfer, a mechanism in which the long hydrogen bond network through the channel could play a key role. Alternatively, the facilitated diffusion of di-oxygen through the channel suggests that singlet di-oxygen could be the principal cause of specific CALI of fused proteins. The entry of di-oxygen through the channel probably also accounts for the high susceptibility of KillerRed to photobleaching.