Proteins that have sequence homology with known RNA m(5)C methyltransferases contain two conserved cysteines, each of which lies within a sequence that bears similarity to a methyltransferase active site. Other enzymes that transfer a methyl group to carbon 5 of a pyrimidine nucleotide, such as the bacterial DNA m(5)C methyltransferases, utilize their single conserved cysteine residue to form a covalent Michael adduct with carbon 6 of the pyrimidine ring during catalysis. We present a model for the utilization of two cysteines in catalysis by RNA m(5)C methyltransferases. It is proposed that one thiol acts in a classical fashion by forming a covalent link to carbon 6 of the pyrimidine base, while the other cysteine assists breakdown of the covalent adduct. Therefore, alteration of the assisting cysteine is anticipated to stabilize the covalent enzyme-RNA intermediate. The model was conceived as a possible explanation for the effects of mutations that change the conserved cysteines in Nop2p, an apparent RNA m(5)C methyltransferase that is essential for ribosome assembly and yeast viability. Evidence for the predicted accumulation of protein-RNA complexes following mutation of the assisting cysteine has been obtained with Nop2p and a known tRNA m(5)C methyltransferase called Ncl1p (Trm4).