The biochemistry and molecular biology of nitrification are poorly understood, almost certainly related to the difficult problem of growing large enough quantities of cells from which to prepare vesicular membranes and purified proteins. This chapter explains the biochemistry and molecular biology of nitrification. Nitrosomonas and Nitrobacter depend on a chemiosmotic mechanism of energy transduction. Many of the special biochemical features of Nitrosomonas and Nitrobacter need to be understood in the context of the ability of the electron transport system to catalyze reversed electron transfer. The demonstration of H_ pumping by intact cells fed with electrons from the nonphysiological donor ascorbate can be taken as support for the H_ pumping activity. The genome sequence clearly shows two reading frames, designated NorA and NorB on the basis of earlier partial sequence information. Bioenergetic arguments have suggested a location at the cytoplasmic surface, but immunolabeling studies have indicated the opposite. The oxidation of ammonia to NO2- by Nitrosomonas is not a straightforward process. The idea that ubiquinol provides electrons for the ammonia mono-oxygenase is supported by the fact that partially purified preparations of the enzyme can use duroquinol as electron donor.