Flavonoids consist of a large family of compounds, which has been estimated to be more than 10,000 compounds. The structural diversity of these compounds comes from different modification reactions. The O-methylation reaction is one of the most important modification reactions of flavonoids and the resulting O-methylated flavonoids have been shown to display new biological activities. The regioselective and substrate specific O-methylation is mediated by O-methyltranferases (OMTs). To date, 30 flavonoid OMTs (FOMTs) have been biochemically characterized from various plants. FOMTs utilize common reaction mechanisms to transfer a methyl group to the hydroxyl group of the flavonoid. Phylogenetic tree analysis along with biochemical characterization of FOMTs provides clues about their substrate specificity and regioselectivity. FOMTs can be used for the production of O-methylated flavonoids that have a particular biological activity.