Abstract: Plant microRNAs (miRNA) act as important regulators of gene expression and carry potential uses in plant genetic engineering. Lignin is an abundant biopolymer in plants, conferring strength to the cell wall. Most of the recalcitrance of the lignocellulosic biomass to produce biofuels is due to the chemical nature of lignin and its interaction with the other components of the cell wall. Thus, understanding lignin biosynthesis and deposition is crucial for the biofuel industry, and interfering in RNA (iRNA) may be a valuable tool to produce transgenic plants with reduced lignin concentration and/or modified composition. Here we report on the miRNA profile of Eucalyptus grandis and E. globulus in which 28 conserved and 19 novel miRNAs were found. We identified 316 putative targets of known and 110 putative targets of novel miRNAs. No significant differences in miRNA expression were found between tension and opposite wood samples. Gene Ontology enrichment analysis returned several attractive targets for identified miRNAs, among which are laccases and transcription factors that may regulate the expression of lignin biosynthesis Ver menos