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While gaining popularity worldwide, botanical products are facing the challenge of product quality and safety. Authentication and quality control of medical herbs have become critical issues. Since DNA composition for a living organism remains consistent throughout development and is not affected by various environmental conditions, DNA profiling can specifically identify a herb species or cultivar, to ensure its quality if there is linkage of its genetic identity with either chemical constituents or bioactivities and to ensure the genetic uniformity of herb materials. Among the many techniques, Amplified Fragment Length Polymorphism (AFLP) and Simple Sequence Repeat (SSR or microsatellite) are gaining popularity due to their high level of polymorphism, reliability and robustness. DNA sequencing of rDNAs, internal transcribed spacers (ITS) and chloroplast genes have also been used. While DNA profiling has been used successfully in differentiating authenticated herbs from other related species and adulterants, in finding intra-specific variation and even genetic diversity in a single farm, there has been comparatively less work done on correlating genetic identity with chemical constituents or bioactivities. In view of the fact that no single authentication procedure can be applied to every medical herb, we suggest a holistic approach by combining use of DNA profiling together with chemical profiling and/or biological activity testing for authentication of medical herbs. For the wider adoption and acceptance of DNA profiling, there is a need for international collaboration in gaining access to authenticated specimens, working out standard operating procedures (SOPs) for DNA profiling, sharing DNA profile information and building mechanisms to deposit and gain access to DNAs.