Structures of reaction intermediates of bovine cytochrome c oxidase (CcO) in the reactions of its fully reduced form with O 2 and fully oxidized form with H 2O 2 were investigated with time-resolved resonance Raman (RR) and infrared spectroscopy. Six oxygen-associated RR bands were observed for the reaction of CcO with O 2. The isotope shifts for an asymmetrically labeled dioxygen, 16O 18O, has established that the primary intermediate of cytochrome a 3 is an end-on type dioxygen adduct and the subsequent intermediate (P) is an oxoiron species with FeO stretch ( ν FeO) at 804/764 cm −1 for 16O 2/ 18O 2 derivatives, although it had been long postulated to be a peroxy species. The P intermediate is converted to the F intermediate with ν FeO at 785/751 cm −1 and then to a ferric hydroxy species with ν Fe–OH at 450/425 cm −1 (443/417 cm −1 in D 2O). The rate of reaction from P to F intermediates is significantly slower in D 2O than in H 2O. The reaction of oxidized CcO with H 2O 2 yields the same oxygen isotope-sensitive bands as those of P and F, indicating the identity of intermediates. Time-resolved infrared spectroscopy revealed that deprotonation of carboxylic acid side chain takes place upon deligation of a ligand from heme a 3. UV RR spectrum gave a prominent band due to cis CC stretch of phospholipids tightly bound to purified CcO.