Burmese grapes (Baccaurea ramiflora), an underutilized fruit tree in the Mekong Delta, having the potential for food sources as well as landscape plants. However, their genetic diversity, utilization and identification have not been dealt with in depth. The present paper aims to assess the genetic diversity of Baccaurea ramiflora Lour and distinguish five Baccaurea cultivars based on eight DNA barcode regions: matK, rbcL, psbA-trnH, ycf1b, rpoC1, psbK-1, atpF-H and ITS. DNA of each cultivar was extracted prior to further amplification and sequencing. Sequences were analyzed by to detect variable sites and the phylogenetic tree was constructed by Maximum Likelihood method. The results showed that two plastid intergenic spacers, atpF-H and psbA-trnH could be used for the distinguishing of Ha Chau cultivar with others cultivar. Due to the tree based method, Ha Chau cultivar located on the monophyletic branch with acceptable genetic distance compared to other cultivars. These data could be applied for reliable identification of Ha Chau cultivar from other Baccaurea cultivars in plant authentication.