Objective: To study rDNA ITS (internal transcribed spacers) sequences variation from di erent population of Aquilaria sinensis in main habitat of China. Methods: The rDNA ITS regions of various A. sinensis were ampli ed by PCR method and sequenced, and they were analyzed by means of the software of CLUSTAL and MEGA. Results: The sequences of rDNA ITS region of A. sinensis were reported for the rst time, and the sequences of ITS region were 680bp (ITS1 246bp, 5.8S 163bp, ITS2 271bp). There were 6 variable sites among populations and the genetic distance were 0.0% to 1.1%,which indicated the intraspecific genetic variation was low of A. sinensis. Conclusion: The variation of rDNA ITS sequences can be used to authenticate A.sinensis from di erent geographical regions and their adulterants.