To control the quality of traditional Chinese medicine (TCM) at the molecular level, magnetic microspheres was utilized to extract and purify DNA from TCM for subsequent biological detection. Fe3O4 magnetic microspheres with high magnetic susceptibility, uniform particle size and superparamagnetism were applied in this study as solid absorbents to extract genomic DNA from different TCM samples, such as roots, stems, leaves, flowers, fruits and seeds. The prepared DNA was used in biological identification of Chinese herbal medicines by PCR and random amplified polymorphic DNA (RAPD) technology. Results showed that high-purity DNA (OD260 nm/OD280 nm ranged from 1.6 to 2.0) was obtained by solid-phase extraction with the magnetic microspheres; Salvia miltiorrhiza Bge. was distinguished from Arctium lappa L. by amplifying rpl16 gene fragment; and three random primers could be used in RAPD analysis of four species of Bupleurum.