Previously we have isolated the specific RNA methyltransferase from the nucleoli of Ehrlich ascites tumor cells. The purified enzyme was found to be specific for methylation of C5 position of cytosine residue in ribosomal RNA in vitro (Obara, 1982b). In the present study, we have investigated the recognition mechanisms of RNA structure by this enzyme from the points of view of both primary and secondary structures. Analysis of in vitro methylation product by ribonuclease T1 digestion indicated the methylation-site(s) was limited to a certain number of nonanucleotide. The next experiments with either Sl nuclease or actinomycin D and ethidium bromide suggested that the enzyme modified only cytidine residue in or located close to the double stranded part of RNA. On the other hand, the characterization of analogues of cytidine residue in the RNA at molecular level showed that the methylation of rRNA was inhibited by either cytidine, CDP or CTP, but little inhibition was observed in the presence of cytosine, 5-methylcytidine and CMP.