Secondary amine monooxygenase from Pseudomonas aminovorans grown on trimethylamine has been purified 265-fold to apparent homogeneity. The purified enzyme exhibits a specific activity of 14.7 mumol of NADPH oxidized per min per mg of protein, a native molecular weight of 210,000, and nondisulfide-linked subunits of molecular weight 42,000, 36,000, and 24,000, each of which is required for activity. The enzyme is extremely labile during purification; rapid handling and the presence of 5% ethanol are essential to enzyme stability. Storage at 77 K in the presence of NADH (1 mM) also confers considerable stability to the purified enzyme. The heme prosthetic group in the enzyme has been identified as protoporphyrin IX. The quantification of prosthetic group components reveals the presence of 1.6 mol of flavin as FMN, 2.0 mol of heme iron, 4.0 mol of acid-soluble (nonheme) iron, and 3.6 mol of free sulfide/210,000 molecular weight enzyme. Ferric and ferrous-CO secondary amine monooxygenase exhibit electronic absorption spectra that are very similar to those of analogous myoglobin derivatives and, therefore, quite distinct from parallel forms of cytochrome P-450, the most extensively studied heme iron-containing monooxygenase. Like myoglobin and, again, in contrast to P-450, this enzyme forms a very stable dioxygen complex. In fact, it is this oxygen-bound form of the enzyme that is obtained from the purification procedure. Once again, the absorption spectrum of oxygenated secondary amine monooxygenase is nearly identical to that of oxymyoglobin. The spectroscopic similarities between secondary amine monooxygenase and myoglobin suggest the presence of an endogenous histidine fifth ligand to the heme iron of the enzymes.