Objective: One common problem affecting herbal remedies is the incorrect identification of plants due to almost similar morphological characters. A promising technique to ensure correct identification of herbal medicine is the use of DNA barcoding where the gene markers either from Chloroplast (cpDNA) or Nucleus (nrDNA) are commonly used to authenticate plants. In this study, three chloroplast barcodes; matK, rbcL and trnL-F were evaluated to authenticate 20 selected medicinal plants of Mt. Arayat National Park (MANP), Pampanga, The Philippines. Methods: The genetic materials from the 20 selected medicinal plants were isolated, amplified, sequenced and aligned. All generated DNA barcodes were subjected to Kimura two-parameter model to calculate intergeneric and intrageneric variations while discriminatory power was determined using BLAST, neighbour-joining (NJ) and Wilcoxon two-sample test. Results: The results show 19 plant samples were successfully amplified. However, rbcL gave the highest sequencing success rate and identification rate up to species level over matK and trnL-F. Though, the three-cpDNA barcodes produced monophyletic clades revealing distinct association among species. The intergeneric divergences of rbcL, matK and trnL-F are significantly higher than their respective intrageneric divergences. This means the three-cpDNA barcodes can effectively discriminate one species from another. Conclusion: The order of efficiency among the DNA barcodes is rbcL>matK>trnL-F. Nevertheless, the three-plastid barcodes could be used for practical and accurate authentication of medicinal plants while the baseline data in this study can be used for proper conservation of medicinal plants.