The enzyme is present in organisms capable of oxygenic photosynthesis, which includes plants, algae, and cyanobacteria. Plastid terminal oxidase and alternative oxidase are thought to have originated from a common ancestral di-iron carboxylate protein. Oxygen reductase activity was likely an ancient mechanism to scavenge oxygen in the early transition from an anaerobic to aerobic world. The plastid oxidase first evolved in ancient cyanobacteria and the alternative oxidase in Pseudomonadota before eukaryotic evolution and endosymbiosis events. Through endosymbiosis, the plastid oxidase was vertically inherited by eukaryotes that evolved into plants and algae. Sequenced genomes of various plant and algae species shows that the amino acid sequence is more than 25% conserved, which is a significant amount of conservation for an oxidase. This sequence conservation further supports the theory that both the alternative and plastid oxidases evolved before endosymbiosis and did not significantly change through eukaryote evolution.
There also exist PTOX cyanophages that contain copies of the gene for the plastid oxidase. They are known to act as viral vectors for movement of the gene between cyanobacterial species. Some evidence suggests that the phages may use the oxidase to influence photosynthetic electron flow to produce more ATP and less NADPH because viral synthesis utilizes more ATP.