The use of herbal remedies is very popular in the United States, with >80 million people buying plant-derived preparations that are often highly degraded or potentially contaminated with nonefficacious plant material. A method utilizing DNA-based markers to identify highly fragmented or powdered plant material sold as botanicals in dietary supplements has been developed. By incorporating and streamlining a repair reaction that utilized fill-in and ligation reactions before the PCR steps, it was possible to amplify highly degraded or sheared DNA isolated from powdered plant material removed from over-the-counter capsules. The primers for the internal transcribed spacer (ITS) region of nuclear ribosomal DNA generate a PCR fragment compatible with the sizes of the repaired DNA. Moreover, a large data set in Genbank facilitated subsequent analysis. This method is a relatively rapid and simple system to facilitate the authentication, as well as the monitoring, of the purity of botanicals in dietary supplements, even those that are improperly dried or stored.