Fine regulation of gene expression is partially ensured by microRNAs (miRNAs) in response to external stimuli. They negatively regulate gene expression by targeting the cleavage or inhibit the translation of target messenger RN As (mRNAs). In Hevea brasiliensis, environmental and harvesting stresses are known to affect natural rubber production. Deep sequencing of small RN As was carried out on plantlets, subjected to severe abiotic stress, and on latex from trees affected or not by TPD, using the Solexa technique. By combining the LeARN pipeline, data from the Plant microRNA database (PMRD) and Hevea EST sequences, we identified 68 conserved miRNA families already characterized in other plant species, and 15 putatively novel miRNA families. MiRNA targets were computationally predicted and analysed. Targets involved in rubber biosynthesis, ROS-scavenging systems and ethylene perception and transduction pathway are presented.