BackgroundParis yunnanensis(Melanthiaceae) is a traditional Chinese medicinal plant of significant pharmaceutical importance. Due to previous taxonomic confusion, a congeneric species,Paris liiana, has been mistaken forP. yunnanensisand cultivated on a large scale, leading to the mixing of commercial products (i.e., seedlings and processed rhizomes) ofP. yunnanensiswith those ofP. liiana.This may have adverse effects on quality control in the standardization ofP. yunnanensisproductions. As the lack of PCR amplifiable genomic DNA within processed rhizomes is an intractable obstacle to the authentication ofP. yunnanensisproducts using PCR-based diagnostic tools, this study aimed to develop a PCR-free method to authenticate commercialP. yunnanensisproducts, by applying genome skimming to generate complete plastomes and nrDNA arrays for use as the molecular tags.ResultsBased on a dense intraspecies sampling ofP. liianaandP. yunnanensis, the robustness of the proposed authentication systems was evaluated by phylogenetic inferences and experimental authentication of commercial seedling and processed rhizome samples. The results indicate that the genetic criteria of both complete plastomes and nrDNA arrays were consistent with the species boundaries to achieve accurate discrimination ofP. yunnanensisandP. liinna. Owing to its desirable accuracy and sensitivity, genome skimming can serve as an effective and sensitive tool for monitoring and controlling the trade ofP. yunnanensisproducts.ConclusionThis study provides a new way to solve the long-standing problem of the molecular authentication of processed plant products due to the lack of PCR amplifiable genomic DNA. The proposed authentication system will support quality control in the standardization ofP. yunnanensisproducts in cultivation and drug production. This study also provides molecular evidence to clarify the long-standing taxonomic confusion regarding the species delimitation ofP. yunnanensis, which will contribute to the rational exploration and conservation of the species.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12870-023-04365-x.