Ethylene is commonly used as a latex stimulant of Hevea brasiliensis by application of ethephon (chloro-2-ethylphosphonic acid); however, the molecular mechanism by which ethylene increases latex production is not clear. To better understand the effects of ethylene stimulation on the laticiferous cells of rubber trees, a latex expressed sequence tag (EST)-based complementary DNA microarray containing 2973 unique genes (probes) was first developed and used to analyze the latex gene expression changes at three different time-points after ethephon treatment: 8, 24 and 48 h. Transcript levels of 163 genes were significantly altered with fold-change values ≥ 2 or ≤ –2 (q-value < 0.05) in ethephon-treated compared with control rubber trees. Of the 163 genes, 92 were up-regulated and 71 down-regulated. The microarray results were further confirmed using real-time quantitative reverse transcript-PCR for 20 selected genes. Analysis used the 8, 24 or 48 h control latex RNA samples comparison to the ET stimulated 8, 24 or 48 h latex RNA samples. Each sample included three independent biological replicates, and each replicate comprised the latex collected from six trees.