We have purified two distinct DNA methyltransferases from pea shoot tips and analysed their sequence specificity using synthetic oligodeoxyribonucleotide substrates and chemical sequencing methods. One methylates only CG target sequences, whereas the other methylates only CAG or CTG target sequences. We have found no evidence for methylation of the 5 cytosine in CCG target sequences either in vivo or in vitro. Using amino-acid sequence data, PCR-amplified fragments from conserved sequences and heterologous probes, we have isolated several cDNA clones that react with mRNA molecules of different sizes.