Cytosine methylation is a fundamental epigenetic mechanism for gene-expression regulation and developement in plants. Here, we report for the first time the identification of DNA methylation patterns and their putative relationship with abiotic stress in the tree crop Hevea brasiliensis (source of 99;of natural rubber in the world). Regulatory ssequences of four major genes involved in the mevalonate pathway(rubber biosynthesis pathway) and one general defense-related gene of three high-yielding popular rubber clones grown at two different agroclimatic conditions were analysed for the presence of methylation. We found several significant variations in the methylation pattern at core DNA binding motifs within all the five genes. Several consistent clone-specific and location-sepecific methylation patterns were identified. The difference in methylation patterns observed at certain pivotal cis-regulatory sites indicated the direct impact of stress on the genome and support the hypothesis of site-specific stress-induced DNA methylation. It is assumed that some of the methylation patterns obseved may be involved in the stress-responsive mechanism in plants by which they adapt to extreme conditions. The study also provide clues towards the existence of highly divergent phenotypic characters among Hevea clones despite their very similar genetic make-up. Altogether, the obsservations from this study prove beyond doubt that there exist epigentic variations in Hevea and environmental factors play a significant role in the induction of site-specific epigenetic mutations in its genome.