Abstract: Paeonia suffruticosa also named Moutan that cultivated in five geographic regions during different growth stages were chosen in this study. Biolog and 454 pyrosequencing technology were used to detect the whole microbial activity and fungal diversity for exploring the relationship between the geo-authentic features of the medicinal plant and the rhizosphere microorganism. The results suggest that the value of average well color development (AWCD) from the rhizosphere soil of P. suffruticosa in the five regions at the fo ur growth stage have an increasing tendency. 9 703 operational taxonomic unit (OTU) were obtained from 272 463 high quality sequences according to the similarity of 97% by the pyrosequencing. Fungi in five phyla, twenty-two classes, seventy orders, one hundred and thirty-nine families and two hundred and sixty-six genera were detected in the five regions excluding twelve percent to fifty-eight percent unidentified fungi. They were divided into four branches, i.e. Blastocladiales, Chytridiomycota, Dikarya and Glomeromycetes. Twenty-four genera such as Leptosphaeria were found in the five regions while six genera such as Curvularia were only detected in the geo-authentic regions. The dominant genera were Guehomyces, Exophiala and Fusarium in geo-authentic regions, whereas genus Leptosphaeria, Cryptococcus, Exophiala, Fusarium and Ceratobasidium in non-authentic regions. The results from principal co-ordinates analysis (PCoA) showed that the fungi formations were similar in Tongling and Nanling region at four different growth stages, and the same in Heze at the leaf bud and fruiting stage. According to heatmap analysis, Tongling and Nanling region showed a close similarity in fungal community structures on phylogenetic analysis, while Bozhou, Heze and Luoyang showed the same. In brief, the whole microbial activity was higher in geo-authentic regions than the non-authentic. Fungi in rhizosphere soil of the medicinal peony presented diversity and region specificity. We found not only the abundant new species in the five regions, but also the phylogenetic similarity in the geo-authentic regions.