Mango is one of the most valuable fruiting plant and occupies a crucial position in Vietnam’s agriculture. There are various indigenous mango cultivars which originate from Vietnam. Utilization of DNA barcode for mango authentication is an appropriate solution that overcomes the limitations of morphological-based methods. In this study, 33 samples, representing 19 mango cultivars, were analysed by amplifying and sequencing the internal transcribed spacer (ITS) and maturase enzyme gene (matK). The results showed that these two barcode candidates were amplified successfully in all samples. ‘Hoa Loc’, a high quality and native mango cultivar is discriminated from others by 52 variation sites in ITS sequence analysis, while the result is 27 for matK. The results also revealed that the noncoding sequence, ITS, has high interspecific distance among such cultivars and should be proposed as a promising DNA barcode for mango identification, based on both sequence quality and discrimination power.