The present invention provides fatty alcohol oxidase (FAO) proteins and nucleic acid molecules encoding the FAO proteins. Also provided are analogs, derivatives, and enzymatically active fragments of the FAO proteins. Vectors and host cells comprising the nucleic acid molecules encoding the FAO proteins, analogs, derivatives and enzymatically active fragments thereof are also provided. In addition, FAO signature peptides and isolated nucleic acid molecules encoding the signature peptides are provided by the present invention. Methods of producing or increasing production of a subject FAO protein, methods for increasing aldehyde production during the second step of the .omega.-oxidation pathway of fatty acids, methods for increasing production of a ketone from an alcohol during the second step of the .omega.-oxidation pathway of fatty acids, and methods for increasing production of a dicarboxylic acid are also provided.