Ethephon, an ethylene generator, stimulates both latex flow and regeneration. Given ethylene triggers the expression of numerous genes in latex cells, a transcriptomics approach was taken in order to understand the molecular mechanisms underlying latex production controlled by this hormone. Two cDNA libraries were constructed using Suppression Subtractive Hybridization (SSH) technology from 4-year-old trees of clone PB 260 in their immature period without stimulation or stimulated with 2.5% ethephon stimulated. Among 1158 sequenced clones, 158 unique transcripts were identified. Putative functions were assigned by sequence analysis using BLASTX, which showed a large number of genes related to transcription and protein synthesis, unknown functions or defence proteins. A high density filter was completed with genes involved in latex metabolism such as rubber biosynthesis and ROS-scavenging protein. Macro-array analysis revealed a general differential expression between clones with a contrasting metabolism. A large proportion of genes was up-regulated for the active metabolic clone PB 260, and by contrast, a down-regulation was observed for lower metabolisms such as PB 217 or RRIM 600. Discrimination of the response to ethylene for these clones was significant for 35 genes, and 5 of them might discriminate between the responses of the 3 clones. The differential gene expression by Real Time PCR upon ethylene stimulation was confirmed for some of these candidate genes. These genes could be used as markers of expression under stress in a marker-assisted selection programme.