Natural rubber (cis-1,4-polyisoprene) is a product of the isoprenoid biosynthesis pathway which requires an allylic pyrophosphate and isopentenyl pyrophosphate (IPP) to initiate and elongate the rubber molecule. The biosynthesis of IPP occurs via two distinct routes: the mevalonate (MVA) and methylerythritol phosphate (MEP) pathways. In this study, the expression of 34 genes related to rubber biosynthesis were compared between high and low latex yielding trees of two rubber tree clones, PB 217 and PB 260. Almost all tested genes revealed no significantly differential expression related to latex yield. Only mitochondrial pyruvate dehydrogenase (PDCE1) showed specific up-regulation in the high latex yielding trees of both tested clones. Interestingly, the expression of PDCE1 involving in the production of acetyl-CoA in mitochondria was also significantly induced by latex loss upon tapping. The increasing of acetyl-CoA and energy production may favor rubber tree to produce more latex. The in silico analysis showed that HbPDCE1 promoter contained ethylene and copper-responsive elements. Ethylene is worldwide used rubber stimulant while copper sulfate was also reported to be able to stimulate the latex yield. This suggested that HbPDCE1 may be transcriptionally regulated by these two compounds however the in vivo regulation of this gene should be further investigated.