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This study focused on the microbiota and chemical compounds of the fermented Pinelliae Rhizomaproduced in Longchang (LC), Zizhong (ZZ) and Xindu (XD), in Sichuan Province (China). High-throughput sequencing was used to analyze the microbiota. GC-MS and LC-MS were used to detect the compounds produced during the three different Pinelliae Rhizomafermentation processes. The bacteria and fungi of the three fermented Pinelliae Rhizomadiffered substantially, with the bacterial content mainly composed of the Bacillusgenus, while the common fungi were only included in four OTUs, which belong to three species of Eurotiomycetesand Aspergillus cibarius. 51 volatile compounds were detected; they varied between LC, XD, and ZZ fermented Pinelliae Rhizoma. C10 and C15 terpenes were most frequently detected, and only curcumene and β-bisabolene were detected in the three fermented Pinelliae Rhizoma. 65 non-volatile compounds were detected by LC-MS, most were of C16, C18, C20, C21 and C22 structures. Cluster analysis showed more similarity between LC and XD fermented Pinelliae Rhizomawith regards to volatile compound content, but more similarity between the XD and ZZ fermented Pinelliae Rhizomafor non-volatiles. Moreover, no correlation between geographical distance and microflora or compounds of fermented Pinelliae Rhizomawas observed. These results showed that hundreds of compounds are produced by the natural mixed fermentation of Pinelliae Rhizoma, and may mostly relate to the microorganisms of five species.