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Abstract Aims and backgroundThe resurrection plantMyrothamnus flabellifoliatolerates complete desiccation and is a great model for studying how plants cope with extreme drought. Root-associated microbes play a major role in stress tolerance and are an attractive target for enhancing drought tolerance in staple crops. However, how these dynamics play out under the most extreme water limitation remains underexplored. This study aimed to identify bacterial and fungal communities that tolerate extreme drought stress in the bulk soil, rhizosphere, and endosphere ofM. flabellifolia. MethodsHigh-throughput amplicon sequencing was used to characterise the microbial communities associated withM. flabellifolia. ResultsThe bacterial phyla that were most abundant across all compartments wereAcidobacteriota, Actinobacteriota, Chloroflexota, Planctomycetota,andPseudomonadota, while the most abundant fungal phyla wereAscomycotaandBasidiomycota. Although the bulk soil hosted multiple beneficial root-associated microbes, the rhizosphere compartment showed the highest functional diversity of bacteria and fungi. In contrast, the endosphere exhibited a low abundance and diversity of microbes. These findings share consistent with the theory thatM. flabellifoliarecruits soil microbes from the bulk to the rhizosphere and finally to the endosphere. It is possible that these microbes could promote drought tolerance in associated plant tissues. ConclusionWe find that compartments act as the major driver of microbial diversity, but the soil physicochemical factors also influence microbial composition. These results suggest that the root-associated microbiome ofM. flabellifoliais highly structured and may aid in plant function.