In response to the stress of harvesting latex due to the stimulation and tapping, a change in the distribution of small RNAs has been observed in latex cells associated with physiological disorders that stop latex flow (Tapping Panel Dryness, TPD). Small RNAs are negative regulators of gene expression either at the transcription level (class size 23-25 nt) or at the post-transcriptional one (class size 20-22 nt). We observed a major peak of 24 nt of small RNA in the latex healthy trees and 21 nt in TPD-affected trees. Our first objective is to annotate small RNAs produced in the latex of TPD-affected trees. In that aim, the MIR genes and miRNAs were annotated for the genome sequence from clone PB 260, as well as transposable elements (TEs). Our results showed that the small 21-nt RNAs accumulating in the latex of TPD-affected trees were not miRNA, derived from MIR genes, and could therefore be siRNAs. TEs have been annotated and represent 74% of the genome sequence of Hevea clone PB 260. Our second objective was to evaluate the contribution of post-transcriptional gene silencing by a small RNA. We sequenced of all 3' ends mRNA degradation products from 6 tissues, subjected or not to abiotic stress and TPD to build an atlas of the small RNA-mediated post-transcriptional regulation of gene expression. Latex cells showed the highest level of post-transcriptional regulation by mRNA cleavage. As a biological perspective, the annotation of MIR genes, transposable elements associated with curated structural and functional annotations, and the consideration of small RNA interference in the regulation of gene expression, will help us to understand the complexity of gene expression regulation networks genome-wide in response to stress.