Flax dew-retting is a key step in the industrial extraction of fibers from flax stemsand is dependent upon the production of a battery of hydrolytic enzymes producedby micro-organisms during this process. To explore the diversity and dynamics ofbacterial and fungal communities involved in this process we applied a high-throughputsequencing (HTS) DNA metabarcoding approach (16S rRNA/ITSregion, IlluminaMiseq) on plant and soil samples obtained over a period of 7 weeks in July andAugust 2014. Twenty-three bacterial and six fungal phyla were identified in soilsamples and 11 bacterial and four fungal phyla in plant samples. Dominant phylawere Proteobacteria, Bacteroidetes, Actinobacteria, andFirmicutes (bacteria) andAscomycota, Basidiomycota, and Zygomycota (fungi) all of which have been previouslyassociated with flax dew-retting except for Bacteroidetes and Basidiomycota thatwere identified for the first time. Rare phyla also identified for the first time in thisprocess included Acidobacteria, CKC4, Chlorobi, Fibrobacteres, Gemmatimonadetes,Nitrospirae and TM6 (bacteria), and Chytridiomycota (fungi). No differences in microbialcommunities and colonization dynamics were observed between early and standard flaxharvests. In contrast, the common agricultural practice ofswath turning affects bothbacterial and fungal community membership and structure instraw samples and maycontribute to a more uniform retting. Prediction of community function using PICRUStindicated the presence of a large collection of potential bacterial enzymes capable ofhydrolyzing backbones and side-chains of cell wall polysaccharides. Assignment offunctional guild (functional group) using FUNGuild software highlighted a change fromparasitic to saprophytic trophic modes in fungi during retting. This work provides the firstexhaustive description of the microbial communities involved in flax dew-retting and willprovide a valuable benchmark in future studies aiming to evaluate the effects of otherparameters (e.g., year-to year and site variability etc.) on this complex process.