The full-length cDNA encoding chromomethylase methyltransferase (CMT), designated HbCMT，was isolated from rubber tree by using PCR and RACE techniques. HbCMT was 2697 bp in length and contained an open reading frame of 2556 bp. Sequence analysis revealed that the ORF of HbCMT encode 851 amino acid residues with a total predicted molecular mass of 95.67 kD. The deduced amino acid sequences of HbCMT showed high identities of 77％、74％、72%、67%、64%和52% to those of the CMT from Theobroma cacao, Cucumis sativus, Cicer arietinum, Solanum lycopersicum and Arabidopsis thaliana. Real time quantitative PCR analysis showed that the transcripts of the HbCMT were differentially expressed in the root, the bark, the leaf and the latex of rubber tree. HbCMT transcript expressed at different levels with the lower in self-rooting juvenile clones than in their donor clones.