Plant S-adenosyl-L-methionine-dependent methyltransferases (SAM-Mtases) are the key enzymes in phenylpropanoid, flavonoid and many other metabolic pathways of biotechnological importance. Here we compiled the amino acid sequences of 56 SAM-Mtases from different plants and performed a computer analysis for the conserved sequence motifs that could possibly act as SAM-binding domains. To date, genes or cDNAs encoding at least ten distinct groups of SAM-Mtases that utilize SAM and a variety of substrates have been reported from higher plants. Three amino acid sequence motifs are conserved in most of these SAM-Mtases. In addition, many conserved domains have been discovered in each group of O-methyltransferases (OMTs) that methylate specific substrates and may act as sites for substrate specificity in each enzyme. Finally, a diagrammatic representation of the relationship between different OMTs is presented. These SAM-Mtase sequence signatures will be useful in the identification of SAM-Mtase motifs in the hitherto unidentified proteins as well as for designing primers in the isolation of new SAM-Mtases from plants.