Halometabolites are compounds that are commonly found in nature and they are produced by many different organisms. Whereas bromometabolites can mainly be found in the marine environment, chlorometabolites are predominately produced by terrestrial organisms; iodo- and fluorocompounds are only produced infrequently. The halogen atoms are incorporated into organic compounds by enzyme-catalyzed reactions with halide ions as the halogen source. For over 40 years haloperoxidases were thought to be responsible for the incorporation of halogen atoms into organic molecules. However, haloperoxidases lack substrate specificity and regioselectivity, and the connection of haloperoxidases with the in vivo formation of halometabolites has never been demonstrated. Recently, molecular genetic investigations showed that, at least in bacteria, a different class of halogenases is involved in halometabolite formation. These halogenases were found to require FADH2, which can be produced from FAD and NADH by unspecific flavin reductases. In addition to FADH2, oxygen and halide ions (chloride and bromide) are necessary for the halogenation reaction. The FADH2-dependent halogenases show substrate specificity and regioselectivity, and their genes have been detected in many halometabolite-producing bacteria, suggesting that this type of halogenating enzymes constitutes the major source for halometabolite formation in bacteria and possibly also in other organisms.