Aquilaria LAM. is an endangered tropical tree that produces agarwood, a common ingredient in medicine, perfumes and incense. The species endemic to China, Aquilaria yunnanensis , is often misidentified as the two valuable species, Aquilaria sinensis and Aquilaria crassna . In present study, three DNA barcodes (internal transcribed spacer (ITS), maturase K gene ( mat K) and trn L- trn F) were used to evaluate whether these genes can be used to discriminate the three species, and evaluate the phylogenetic relationship between the three Aquilaria species. For accurate identification of the three Aquilaria species, a total of 26 nucleotide variations were detected when comparing the three DNA barcodes. We found that A. sinensis is closely related to A. crassna based on combination of nuclear and chloroplast DNA barcodes, and is closely related to A. yunnanensis based on chloroplast DNA barcodes. Taken together, we suggest that the combination of ITS+ mat K and ITS+ trn L- trn F are suitable for identifying these three Aquilaria species.