show Abstracthide AbstractTraditional Chinese medicine (TCM) has been practiced for thousands of years, but only within the last few decades has its use become more widespread outside of Asia. Concerns continue to be raised about the efficacy, legality and safety of many popular complementary alternative medicines, including TCMs. Ingredients of some TCMs are known to include derivatives of endangered, trade-restricted species of plant and animal and therefore contravene the Convention on International Trade in Endangered Species (CITES) legislation. Chromatographic studies have detected the presence of heavy metals and plant toxins within some TCMs, and there are numerous cases of adverse reactions. It is in the interests of both biodiversity conservation and public safety that techniques are developed to screen medicinals like TCMs. By generating over 47,000 amplicon sequence reads from 15 TCM samples presented in the form of powders, tablets, capsules, bile flakes and herbal tea, targeting both chloroplast (trnL) and mitochondrial (16S ribosomal RNA) genes, we show that Second Generation, high-throughput sequencing (HTS) of DNA represents an effective means to audit the ingredients of TCMs. Comparison of DNA sequence data to reference databases, revealed the presence of 60 different plant families, and included genera, such as Ephedra and Asarum, which are potentially toxic. Similarly, six animal families were identified, that include four genera that are classified as vulnerable, endangered, or critically endangered, including Asiatic black bear (Ursus thibetanus), black musk deer (Moschus fuscus), Siberian musk deer (Moschus moschiferus), and Saiga antelope (Saiga tatarica). Bovidae, Suidae, and Bufonidae DNA were also detected in many of the TCM samples, and were rarely declared on the product packaging. This study demonstrates that deep sequencing via HTS is an efficient and cost-effective way to audit highly processed TCM products and will assist in monitoring their legality and safety.