The rhizome of Actaea racemosa L., commonly called black cohosh, is a popular botanical dietary supplement used to treat female health concerns. The rhizomes used in black cohosh products are often collected from the wild. To ensure quality control, it is imperative that plants be correctly identified. This paper examines the use of the DNA fingerprinting technique, AFLP, as an analytical means of identifying A. racemosa from three other closely related sympatric species. To this end, 262 AFLP markers were generated, and one unique fingerprint was identified for A. racemosa, whereas two, six, and eight unique fingerprints were identified for the closely related species A. pachypoda, A. cordifolia, and A. podocarpa, respectively. Two commercial black cohosh products were also subjected to AFLP analysis and shown to contain only A. racemosa. The results of this study suggest that AFLP analysis may offer a useful method for quality control in the botanical dietary supplements industry.