Gastrodia elata Blume has been recognized as a precious herbal medicine for thousands years due to its abundant bioactive ingredients and health-promoting features. The inadvertent or intentional adulteration of G. elata poses a severe crisis for consumers and significantly disrupts the market order. Therefore, accurate discrimination of G. elata from its adulterants is crucial to ensure its therapeutic effects and protect consumers’ interests. In this study, two species-specific PCR assays for molecular discrimination of G. elata from its five adulterants were established by targeting the chloroplast rps12 and clpP regions, respectively. Both of the assays can reliably identify as little as 0.1 % of deliberate adulteration with a detection threshold of only 0.01 ng of template DNA, and the assays are effective in detecting adulteration within G. elata as well as its commercial extracts. The present study provide a highly sensitive and reliable method for ascertaining the authenticity of G. elata and its commercial products, and the methodology can be employed in the authenticity and adulteration detection of other herbal products.