In response to environmental cues and latex harvesting stress, Hevea revealed an alteration in sRNA transcriptome in latex cells associated with physiological disorders halting latex flow (Tapping Panel Dryness, TPD). Most sRNAs are 24 nt in healthy trees and 21 nt in TPD-affected trees. This questions the contribution of post-transcriptional gene silencing by sRNA to TPD. Firstly, MIR genes and miRNAs were annotated. Secondly, degradome data were used to highlight sRNA-mediated post-transcriptional genome expression regulation in response to abiotic stress and TPD. We sequenced all 3' ends of degraded mRNAs from 6 tissues, subjected or not to abiotic stress/TPD, in order to validate all sRNA-based target cleavage sites simultaneously. Our results showed that the 21-nt sRNAs accumulating during TPD were not derived from MIR genes and could therefore be classified as siRNAs, and correspond to epigenetically-activated siRNA (easiRNA). From “degradome” analysis from 6 distinct tissues, latex cells displayed the highest level of post-transcriptional regulation by mRNA cleavage. Interestingly, natural rubber biosynthetic pathway is under a strong post-transcriptional silencing. Genes involved in miRNA biogenesis were identified and the analysis of their sequences revealed a recent duplication of Argonaute (AGO) and Dicer-like (DCL) families in Hevea genome, consistent with the whole genome duplication shared with cassava. Partial conservation of miRNA-mediated post-transcriptional regulation was observed between Hevea and Arabidopsis. Discovery of miRNA/target couples through “degradome” analysis, annotation of MIR genes and transposable elements, representing more than 70% of the Hevea genome sequence and interspersed between coding genes, can lead to a full comprehensive picture of post-transcriptional and transcriptional regulations of gene expression by sRNA at genome-wide level.