According to Chinese Pharmacopoeia (2010ed), Chishao,Paeoniae Radix Rubra and Baishao,Paeoniae Radix Alba are both from the root of Paeonia lactiflora Pall. In recent years, it is known from the studies that Chishao and Baishao must have the resemblance in the chemical composition, but the differences have related to the ecological environment and the processing methods, this makes their functions be different, athough they derive from the same original plants. This review explores the material basis and functions differences based on the analysis of the relationship in Chishao and Baishao on characteristic index function and the genetic background and the analysis of the clinical and pharmacological effects. It may provide more scientific data for identification and establishment of new quality control methods of the Paeoniae Radix Alba and Paeoniae Radix Rubra in the future.