Two kinds of peony roots--white peony root (WPR) and red peony root (RPR)--are used for different remedies in traditional Chinese medicine; however, most of them are derived from the same botanical origin, Paeonia lactiflora. The difference between WPR and RPR has been debated for a long time. This study attempted to clarify the genetic and chemical characteristics of WPR and RPR in order to provide a scientific dataset for their identification and effective use. The nucleotide sequence of nrDNA internal transcribed spacer (ITS) and the contents of 8 main bioactive constituents were analyzed from specimens of P. lactiflora, P. veitchii and two related species as well as crude drug samples of WPR, RPR and peony root produced in Japan. Of the samples derived from P. lactiflora, the WPR produced in the southern parts of China and the RPR produced in the northern parts of China were clearly divided into two subgroups within the P. lactiflora group based on similarity of the ITS sequences. The nucleotides at positions 69, 458 and 523 upstream of the ITS sequence served as molecular markers to discriminate between WPR and RPR. Quantitative analysis indicated that the RPR samples obviously contained a higher content of paeoniflorin and paeonol, but a lower content of albiflorin than the WPR produced in the southern parts of China and peony root produced in Japan. The WPR available from Chinese markets was usually processed by sulfur fumigation, which resulted in an extremely low content of paeoniflorin. This study indicated that WPR and RPR were not only geographically isolated, but also genetically and chemically separated. The ITS sequence provided a genetic index for their identification.