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The purpose of this study was to compare the composition and stability of bacteria and fungi communities during the propagation of sourdoughs prepared with organic or conventional whole wheat (Triticum aestivum) flours from South Brazil.Sourdoughs were prepared and samples were collected during different fermentation times (0 to 216 h). Total DNA of sourdough samples were extracted and the 16S rRNA gene and Internal Transcribed Spacer region were sequenced by MiSeq-Illumina. A total of 43 and 56 OTUs were identified and defined as core taxa in the bacterial and fungal communities, respectively. The analysis revealed increases in the relative abundances of the lactic acid (Pediococcus pentosaceus, Weissella hellenica and Limosilactobacillus pontis) and acetic acid bacteria (Gluconobacter frateurii and Acetobacter tropicalis)during the sourdough propagation. The filaments fungi, Alternaria tenuissima, Fusarium culmorum, Fusarium petersiae and Microdochium seminicola remained more stable in organic than conventional during propagation cycles. After 216 h of fermentation, both sourdoughs were dominated by acid-and salt-tolerant yeast Issatchenkia orientalis (syn Pichia kudriavzevii, and Candida glycerinogenes). In conclusion, there were no significant differences in microbial communities among the sourdough samples. This study revealed that both flours contain autochthonous LAB, AAB, and yeasts with biotechnological applications in sourdough bread-making.