Abstract: To build up a stable and easy doing method for molecular identification in traditional Chinese medicine, on basis of RAPD, the new method mainly changed the primer length and PCR annealing temperature. Panax ginseng, Panax quinquefolius and its nine adulterants were used to establish the method and test it using MARMS primers published in 2004. The new method also used to authenticate Chinese Materia Medica of Tian-hua-fen (Radix Trichosanthes) and Bai-zhi (Radix Angelica). Primer Pg-q36F obtained polymorphic bands of P.Ginseng, P.quinquefolius and its adulterants. The identification result is identical to that published before and more stable. Primer TkS1-64F obtained polymorphic bands of Tian-hua-fen and its nine adulterants. Primer AfS1-100F obtained polymorphic bands of Bai-zhi and its three adulterants. The method has good stability and reproducibility and can easily identify authertic medicines from their adulterants. It was a potential molecular method to identify other Chinese Materia Medica. The method was named as anchored primer amplification polymorphism DNA (APAPD).