Burmese grape  (Baccaurea ramiflora  Lour.)  is  an underutilized fruit tree in the Mekong Delta  and  has the potential for food sources as well as landscape plants, especially Ha Chau cultivar. It has been considered an indigenous plant in Can Tho city, Vietnam with specific taste.  However, their genetic diversity, utilization,  and identification have not been dealt with in-depth. This  study   aimed to  characterize genetic diversity among the five cultivars of  Burmese  grape  in the Mekong Delta and  to distinguish  Ha Chau from other  cultivars based on DNA barcodes, namely   matK,  rbcL,  ycf1b,  rpoC1,  psbK-I,  atpF-H,  and ITS. DNA of  twelve individuals belong to five  Burmese grape  cultivars  was extracted prior to further amplification and sequencing. Sequences were analyzed to detect variable sites and the phylogenetic tree was constructed by  the  Maximum Likelihood method.  Based on  substitution sites and indel mutations,  the  plastid intergenic spacer atpF-H and ycf1b gene reflected the genetic diversity in five Burmese grape cultivars. Moreover, these sequences were valuable  DNA barcodes  for  discrimination  of Ha Chau  cultivar. In combination  of  four markers (rbcL,  rpoC1,  ycf1b,  and  psbK-I)  for phylogenetic construction,  our  finding  revealed that  Ha Chau cultivar  is  closely related to  Red cultivar with  highly  supported  bootstrap value of  89%.  Such  data could be applied for reliable identification of Ha Chau cultivar from other  B.  ramiflora  cultivars in plant authentication.