In order to isolate high-quality genomic DNA from medicinal plant tissues enriching polyphenols and polysaccharides, a simple and rapid method based on CTAB extraction for isolating high-quality intact DNA was established by modifying several existing methods. With this technique, the absorbance ratio (A260/A280) of DNAs obtained from fresh and/or dried roots of Panax ginseng, P. Quinquefolius and P. notoginseng was 1.8 approximately. The restriction fragments of DNAs were directly digested with restriction enzyme (EcoR I/Mse I), linked up by T4 DNA ligase and amplified by nested PCR. Reproducible amplified fragment length polymorphism (AFLP) genomic DNA fingerprinting profiles were established with the isolated DNAs. The results demonstrate that the modified technique may be efficient and reliable in isolating high-quality and high-molecular-weight DNAs from fresh and/or dried medicinal plants containing a high content of polyphenols and polysaccharides. We expect that this method can also be applied to other plants.