AbstractBACKGROUND: Food adulteration remains a major global concern. DNA fingerprinting has several advantages over chemical and morphological identification techniques. DNA microarray‐based fingerprinting techniques have not been used previously to detect adulteration involving dried commercial samples of closely related species. Here we report amplification of low‐level DNA obtained from dried commercial ginseng samples using the Qiagen™ REPLI‐g® Kit. Further, we used a subtracted diversity array (SDA) to fingerprint the two ginseng species, Panax ginseng and Panax quinquefolius, that are frequently mixed for adulteration.RESULTS: The two ginseng species were successfully discriminated using SDA. Further, SDA was sensitive enough to detect a deliberate adulteration of 10% P. quinquefolius in P. ginseng. Thirty‐nine species‐specific features including 30 P. ginseng‐specific and nine P. quinquefolius‐specific were obtained. This resulted in a feature polymorphism rate of 10.5% from the 376 features used for fingerprinting the two ginseng species. The functional characterization of 14 Panax species‐specific features by sequencing revealed one putative ATP synthase, six putative uncharacterized proteins, and two retroelements to be different in these two species.CONCLUSION: SDA can be employed to detect adulterations in a broad range of plant samples. Copyright © 2011 Society of Chemical Industry