DNA barcoding is currently gaining popularity due to its simplicity and high accuracy as compared to the complexity and subjective biases associated with morphology-based identification of taxa. The standard chloroplast DNA barcode for land plants recommended by the Consortium for the Barcode of Life (CBOL) plant working group needs to be evaluated for a wide range of plant species. The present study therefore tested the potential of the rbcL and matK marker for the identification of mangrove plants belonging to diverse families of coastal regions. Here, DNA barcoding is being used to identify mangrove plants found in Kerala and distinguished them from other similar species. Several challenges to the successful implementation of plant DNA barcoding are presented and discussed. Despite these challenges, DNA barcoding has the potential to uniquely identify mangrove plants and provide quality control and standardization of the plant material supplied to the pharmaceutical industry.