Background: The Philippines is home to some ethnomedicinal Apocynaceae that has been used to cure common ailments. They are perceived to be safe, but misidentification can lead to substitution and adulteration. Morphological characters are primarily utilized to identify these species but a new method utilizing molecular characters called DNA barcoding has emerged. In this study, the efficiency of matK, rbcL, trnH-psbA, and trnL-F to molecularly authenticate selected Apocynaceae species were tested. Materials and Methods: Genomic DNA from silica-dried leaf samples were isolated and used as a template for generating DNA barcodes. Pair-wise sequence divergence using Kimura-2-Parameter was used to analyze inter-specific and intraspecific variations among the barcodes, whereas basic local alignment search tool (BLAST) and neighbor-joining (NJ) analyses were employed to examine discrimination success. Results: The results show that matK is the best barcode for Apocynaceae as it has the highest amplification and sequencing success together with rbcL while having high inter-specific and low intra-specific divergence relative to the other candidate barcodes. Furthermore, matK provided the highest discrimination both in BLAST and NJ analyses. Conclusion: This study proposes the use of matK as the principal barcode for Apocynaceae.