A HPLC method was established to determine the contents of the five anthraquinones and rhaponticin in the different varieties of Rhei Radix et Rhizoma. The difference existed in different varieties. The results showed that rhein and rhaponticin were marker substances which could be used to distinguish palm leaf groups rhubarb and wave leaf groups rhubarb. Authentic rhubarb didn't contain rhaponticin. Falsify rhubarb contains trace amounts of rhein. Rheum tanguticum contains abundant rhein. The ratio value of the content of rhein to chrysophanol could be used to distinguish R. tanguticum from the other two authentic varieties (R. palmatum and R. officinale). The content of rhaponticin varied largely in different varieties of wave leaf groups rhubarb.