The medicinal tree peony (Paeonia suffruticosa) is an important resource in traditional Chinese medicine. Soil bacteria, especially rhizosphere bacteria, have strong effects on plant health and growth. In this study, the bacterial community structure and diversity in P. suffruticosa rhizosphere soil in five major distribution areas in China were investigated by amplified ribosomal DNA restriction analysis (ARDRA). The ARDRA patterns of the amplified 16S rRNA gene produced an average of 2-6 bands that ranged in size from 100 to 1302 bp, which indicated that the fragments of the 16S rRNA gene were efficiently double-digested with the restriction endonucleases HinfI and Csp6I. ARDRA-based cluster analysis showed that 702 positive clones were clustered into 74, 69, 76, 73, and 72 operational taxonomic units (OTUs) in the FH, YS, BZ, HZ, and LY libraries, respectively. Most of the OTUs contained 1-3 clones, which implied high diversity in the peony rhizosphere soil; twenty-six OTUs contained 4-6 clones; and five OTUs contained 7-12 clones. Rarefaction analysis showed that the positive clones in each library covered the diversity of bacterial taxa, which was further confirmed by clone library coverage (range:71.32%-81.40%). Diversity analysis indicated high bacterial diversity in the soils (Shannon diversity index 3.949-4.184; Chao1 index range 89.52-107.25). Sequence analysis revealed diverse bacterial phyla in the 16S rRNA gene library, consisting of α, β, γ, and δ subclasses of Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia, TM7, Gemmatimonadetes, and three unclassified bacteria. The dominant phyla were Proteobacteria and Acidobacteria (47.34% and 14.36% of the total clones, respectively), and the dominant genera in the clone libraries were Pseudomonas, Burkholderia, and Arthrobacter. In addition, a portion of the clones was only distantly related to sequences in the GenBank database, suggesting that bacteria in rhizosphere soil of the medicinal tree peony were unique and diverse. Furthermore, the relative abundance of Firmicutes (mainly Bacillus spp.) was positively correlated with soil Cu content. The rhizosphere bacteria belonged the same dominant phyla (Proteobacteria, Acidobacteria, and Actinobacteria) and showed high diversity between geo-authentic and non-authentic areas, implying that P. suffruticosa tended to form a similar microenvironment and select similar bacterial communities in the rhizosphere soil.