Life on earth started more than 3.8 billion years ago. The atmosphere and the oceans were under reducing conditions, molecular oxygen was absent. Photosynthesis was invented already about 3.5 billion years ago. It was anoxygenic meaning that molecular oxygen was not produced, hydrogen and hydrogen sulphide were the likely electron donors for photosynthetic electron flow and fixation of carbon dioxide. Then the ancestors of the present day cyanobacteria started to use water as a source for electrons resulting in the release of molecular oxygen into the atmosphere at least 2.8 billion years ago. A significant increase in the atmosphere’s oxygen concentration was only observed about 500 million years later. The appearance of molecular oxygen was the biggest ecological catastrophe which ever happened on earth. Oxygen, in particular in the presence of light and coloured substances, is extremely toxic, and the existing organisms had to invent ways to detoxify oxygen in order to survive. One strategy is to remove molecular oxygen by reducing it to water. There are several soluble enzymes known performing this reaction, e.g. flavohemoproteins in bacteria and yeasts and di-iron flavoproteins in archaea. They are located in the cytoplasm. More important, however, are membrane integrated enzymes, called terminal oxidases, which receive electrons from one side of the membrane, and use protons from the opposite side in order to reduce molecular oxygen to water. As a result of the topologically opposite origin of the charged substrates (electrons and protons) an electric voltage and a pH difference is created across the membrane. This voltage is used e.g. to drive the uptake of nutrients and the formation of the universal biological energy carrier ATP from ADP and inorganic phosphate. Therefore the necessary removal of the waste product oxygen could be converted into an energy supplying reaction. Some terminal oxidases even enhance the energy conversion by “pumping” additional protons across the membrane. The most prominent representatives of the terminal oxidases are the heme-copper oxidases which are found in mitochondria of higher cells and in manybacteria and archaea. The structures of two divergent terminal oxidases, a so-called aa3-type oxidase from an aerobic bacterium, and a cbb3-type from a microaerophilic bacterium will be presented and discussed, in particular in relation to their function as proton pumps.