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Agarwood is a kind of high valued non-timber product a cross A sia，Middle East，and Europe-As the agarwood is form ed only when itsre source trees-the genus Aquilaria are wounded or infected by some microbes．overharvesting and habitat loss are threatening the popul ations of a garwood-producing specles．Thus，revealing the regulation mechanisms of agarwood formation is critical to promote the production efficiency and Drotect the wildre source of Aquilaria species．MicroRNAs(miRNAs)are a group of gene expresslon regulators whion have ove rwhelming effects on alarge spectrum of biological processes．However，little is known a bout the roles of miRNAs in a garwood form ation．In this study,the small RNA high-throughput sequencing and 454 transcriptome data were adoDted to identify miRNAs and monitor their expression under wound treatment in the stems of A．sinensis．By in silico analysis of the small RNA deep sequencing data and transcriptome data．wedi scoveredll conserved miRNAs，160 novelmiRNAs as well as 283 homologues miRNAsinA．sinensis．The expression profile of all miRNA families or individual miRNAs were calculated according to their reads numbers．The miR171，miR390，miR394，miR2111，andmiR3954 families kept the reduced level until 2 days atier the treatrnent examined during the time-course after wound treatment．131 homologious sequences in the 1／2 h library showed over 3-fold variance of read number compared with the control library．12 of them which exhibited strong expression a lterations were further confirmed by real-time quantitative PCR．This not only shows the existence of miRNAs in this A sian economically significant tree species but also indicated its critical role in stress-induced agarwood formation．Target prediction and annotation of the conserved and novel miRNAs demonstrated binding，metabolic process，catalytic activity,and cellularprocess were the most common functions of the targets ofthese newly identified miRNAs in A．sinensis．These results strongly support our proposition that the miRNAs are participated in the stem wound response of Aquilaria species and can influence the metabolic processes which have great potential to include the agarwood formation．