A fully active form of hydroxylamine oxidoreductase from Nitrosomonas has been purified with high recovery and shown by reverse-phase high performance liquid chromatography and N-terminal analysis to contain only a 63-kDa subunit and to lack the 11-kDa protein previously thought to be a second subunit. Based on the previously published values of molecular weight in solution, hydroxylamine oxidoreductase probably has an alpha 2 or alpha 3 oligomeric structure. The enzyme was digested separately with trypsin and chymotrypsin and peptides which contained covalently bound heme were separated by high performance liquid chromatography and their amino acid sequences determined. A total of seven heme-containing peptides of unique amino acid sequence were obtained. Six of these heme-containing peptides clearly contained a single c-heme with optical properties indistinguishable from the tryptic heme-containing peptide from horse heart cytochrome c. No noncovalently bound heme was observed. One of the seven heme-containing peptides (T7) was unusual in that it released 2 amino acid residues after each cycle of the Edman degradation due to a nondisulfide cross-link and exhibited a Soret band that was broadened in both the ferric form at neutral pH and the pyridine ferrohemochrome. Subdigestion of peptide T7 with nonspecific proteases (Pronase, bromelain, or pepsin) resulted in the isolation of two smaller heme-containing peptides of unique sequences. One of these was spectrally identical to the other c-heme containing peptides, whereas the second was still apparently cross-linked, again releasing 2 amino acid residues after each Edman cycle. This second peptide possessed a heme-like chromophore with absorption bands (Soret, alpha and beta) red-shifted about 6 nm relative to the spectrum of c-heme-containing peptides. Thus, hydroxylamine oxidoreductase contains a total of eight covalently bound hemes per subunit, seven of which are c-hemes. The eighth, which is attached to a cross-linked peptide, is probably the unusual P460 heme which is unique to hydroxylamine oxidoreductase and thought to be at the active site.