Proper identification and authentication of medicinal plants are vital for the quality and safety of herbal medications. Morphological and phytochemical-based traditional methods of identification may not suffice in discriminating close relatives, especially in dried, ground and processed herbs. DNA barcoding has emerged as a molecular identification technique that uses genomic loci in differentiating plant species as well as detecting botanical adulteration. This paper reviews the relative performance of three common DNA barcodes; nuclear ribosomal internal transcribed spacer 2 (ITS2) and chloroplast rbcL and matK genes. A structured narrative review was carried out on published literature on amplification and sequencing feasibility, ability of these three DNA barcodes to discriminate plant species, genetic variability, barcode gap properties and the use of the three barcodes in medicinal plant identification. According to published data, the ITS2 is more effective than the other two loci in providing high species discrimination, especially among medicinal plant species while rbcL provides successful amplification and sequencing but with low discrimination power. On the other hand, matK locus provides extra sequence variation with amplification efficiency being dependent on primer compatibility and taxonomy of plants. The findings in the study of medicinal plant species, such as Lamiaceae, provide additional proof that barcoding results can differ greatly depending on the quality of samples, taxonomic groups, database completeness, and identification process. Furthermore, the review stresses the importance of applying species-specific PCR amplification, quantitative PCR amplification, high-resolution melting analysis, and DNA metabarcoding in the detection of adulteration and misidentification in herbal products. However, the problems related to degraded DNA, hybridization, intragenomic polymorphism, primers' preference, and incompleteness of database cannot be overlooked either. Thus, the use of complementary DNA barcodes along with reference samples, validated sequence databases, and phytochemistry is the key.