Monoamine oxidase (MAO) A and MAO B are a crucial pair of isoenzymes, which oxidatively deaminate monoamine neurotransmitters and dietary amines with a production of hydrogen peroxide. These two isoenzymes have different but overlapping substrate and inhibitor specificities. MAO A and MAO B share 70% amino acid sequence identity and show different temporal and spatial expressions in both humans and mice. Abnormal MAO A or MAO B activity has been implicated in numerous neurological and psychiatric disorders. A better understanding of the transcriptional regulation of MAO A and MAO B genes may help explain the differential tissue-specific expression of these two isoenzymes and provide insights into the molecular basis of the disorders associated with MAO dysfunction. This review discusses the recent progress in the transcriptional regulation and multiple functions of MAO A and MAO B genes.