Vanda tricolor Lindl. is one of the important ornamental plants favored by many people in the world. However, this plant required many years for vegetative growth before the first flowers emerge. Since the flower is one of the most important organs in morphological identification, an alternative approach through DNA barcoding is one of the best breaking approaches for fast and accurate identification regardless of floral organs availabilty. In this study, three different primer sets (matK, rbcL, ITS2) were used for molecular identification. DNA isolation was carried out using plant genomic isolation kit and was applied as template in PCR reaction. After confirmation using agarose gel electrophoresis and visualized under UV transilluminator, the PCR products were then purified and subjected for sequencing analysis. The sequences length obtained were 408 bp, 317 bp and 461 bp for matK, rbcL, and ITS2, respectively. Further analysis using BLAST and phylogenetic tree construction revealed that all three primer sets are applicable for identification of Vanda orchids. Notably, the ITS2 sequence showed specificity and able to discriminate up to the species level, thus recommended to be used in molecular identification of Vanda orchids.