Abstract: MicroRNAs (miRNAs) are 20–24 nucleotide long molecules processed from a specific class of RNA polymerase II transcripts that mainly regulate the stability of mRNAs containing a complementary sequence by targeted degradation in plants. In recent years, the rapid development of high-throughput sequencing accelerated the the research of miRNA. This Review discussed the discovery of plant miRNA,current advances of tree miRNAs and the genetic manipulation of amiRNA in trees. Especially, the development of miRNAs research in Populus, fruit trees, eucalyptus, tea, rubber trees, Jatropha tree, Ammopiptanthus mongolicus, and gymnosperms trees were reviewed in detail. Given the increasing number of miRNA, future research would focus on the verification of its functions. Therefore, it is important to summarize the current status of information on miRNAs in trees and to guide future studies on the role of miRNAs in the biology of woody perennials.