The understanding of enzymatic incorporation of halogen atoms into organic molecules has increased during the last few years. Two novel types of halogenating enzymes, flavin-dependent halogenases and alpha-ketoglutarate-dependent halogenases, are now known to play a significant role in enzyme-catalyzed halogenation. The recent advances on the halogenating enzymes RebH, SyrB2, and CytC3 have suggested some new mechanisms for enzymatic halogenations. This review concentrates on the occurrence, catalytic mechanisms, and biotechnological applications of the halogenating enzymes that are currently known.