Uncontrolled and unsustainable trade in natural resources is an increasingly important threat to global biodiversity. In recent years, molecular identification methods have been proposed as tools to monitor global supply chains, to support regulation and legislative protection of species in trade and enhancing consumer protection by establishing whether a traded product contains the species it is purported to contain. Here, we demonstrate the efficacy of a target-capture genomic DNA barcoding method to establish the identity and geographic origin of samples traded as the red-listed medicinal plant Anacyclus pyrethrum. This approach is used to unveil product adulteration and substitution in this herbal medicine s national and international supply chains. The approach outperforms standard plant DNA barcodes and entire plastid genome sequences. This approach offers the potential to achieve routine species-level DNA-based identification including insights into geographic origin. This represents a major development for biodiversity conservation, including the regulation and monitoring of trade in natural plant products.