Visible and UV-resonance Raman spectroscopy was employed to investigate the reaction of NO with cytochrome caa₃ from Thermus thermophilus. We show the formation of the hyponitrite (HO–NN–O)⁻ bound to the heme a₃ species (ν_NN = 1330 cm⁻¹) forming a high spin complex in the oxidized heme a₃ Fe/Cu_B binuclear center of caa₃-oxidoreductase. In the absence of heme a₃ Fe²⁺–NO formation, the electron required for the formation of the NN bond originates from the autoreduction of Cu_B by NO, producing nitrite. With the identification of the hyponitrite intermediate the hypothesis of a common phylogeny of aerobic respiration and bacterial denitrification is fully supported and the mechanism for the 2e⁻/2H⁺ reduction of NO to N₂O can be described with more certainty.