Chuanniuxi (Radix Cyathule) is one of the most important geo-herb in Sichuan province, which adulterants are Hongniuxi (Cyathula capitata) and Huainiuxi (Achyranthes bidentata). In this paper Chuanniuxi and its adulterants were identified by SCAR markers. Nineteen populations from Tianquan, Baoxin, Huili and Jinkouhe were collected and their RAPD fingerprints were established. Based on the RAPD patterns, two polymorphic bands F300 and F500 were selected, recycled, cloned and sequenced. According to the sequences two pairs of sequence characterized amplified regions (SCAR) primers were designed and used to amplify all materials to prove the efficiency of identification of the different populations. Chuanniuxi and Huiniuxi could be distinguished by the primer SC-320, Chuanniuxi and Hongniuxi could be distinguished by the primer SC-495. Combining the two SCAR markers, Chuanniuxi, Hongniuxi and huainiuxi could be identified effectively and quickly.