DNA barcoding is a widely used tool for species identification and authentication. However, it may not be applicable to highly processed herbal products due to severe DNA fragmentation. The emergence of DNA metabarcoding provides an alternative way to solve the problem. In this study, we are the first to combine the use of adaptor ligation-mediated PCR method and metabarcoding to reveal species identities in herbal products. As an illustration, we applied the method on three Hedyotis herbal products collected from China and Thailand. Results showed that H. diffusa and H. corymbosa were present in the products which were consistent with their label claims. Our study indicated that the adaptor ligation-mediated PCR with metabarcoding approach is useful for authentication of highly processed herbal products.