The potential of exploiting the microbiota towards the improvement of plant health to achieve agricultural goals experiences an ever-increasing interest. To do so through plant breeding requires the identification of adaptive host genetic factors affecting the assembly of microbial communities with which they associate. The main goal of the project for which I’ll present some results during the seminar, is to establish a genomic map of local adaptation in Arabidopsis thaliana to bacterial communities in the leaf and root compartments. More precisely, based on 168 natural populations of A. thaliana located in south-west of France, we conducted a Genome–Environment Association (GEA) analysis to finely map adaptive genomic regions of A. thaliana associated with descriptors of bacterial microbiota and pathobiota. To control for correlated environment effects, we also characterized the populations for a set of climate variables, soil agronomic properties and plant community descriptors. A non-negligible fraction of top single nucleotide polymorphisms was associated with both microbiota/pathobiota descriptors and other environmental factors, highlighting the importance of considering the actual abiotic and biotic drivers of bacterial communities to disentangle genetic variants for microbiota/pathobiota adaptation from genetic variants for climate/soil/plant community adaptation. The adaptive loci associated with the presence of bacterial species were highly dependent on the identity of the bacterial species, suggesting a high degree of biotic specialization of A. thaliana to members of its microbiota/pathobiota interaction network. Moreover, the identification of adaptive loci associated with alpha-diversity and composition of bacterial communities supports the ability of A. thaliana to interact simultaneously with multiple bacterial species, which in turn can help to understand the role of community-wide selection. Finally, the candidate genes underlying QTLs were significantly enriched in signaling processes, thereby reinforcing the importance of plant innate immunity to modulate natural adaptive interactions between A. thaliana and its microbiota