There is growing interest in the potential of harnessing the microbiome towards the improvement of plant health to achieve agricultural goals. To do so through plant breeding, requires a better understanding of the role of the host genome in modulating microbiota variation. In particular, there is a need to overcome the current limits on the description of host-microbiota interactions at the genomic and molecular levels. However, the host genetic architecture structuring microbiota is only partly described in plants. To dissect the genetic architecture driving adaptive plant-microbiota interactions, I will present the results of complementary approaches in association genetics applied on Arabidopsis thaliana: (i) a Genome-Environment Association (GEA) analysis on 141 whole-genome sequenced natural populations of A. thaliana characterized in situ for their leaf and root bacterial communities and a large set of non-microbial ecological factors (i.e., climate, soil, and plant communities), and (ii) a Genome-Wide Association study conducted in field conditions on 162 whole-genome sequenced accessions of A. thaliana inoculated with 13 native Plant Growth-Promoting Bacteria (PGPB) isolated from these populations. By combining these two approaches, we established a genomic map of local adaptation in A. thaliana to its native bacterial microbiota. Plant immunity appears as a major source of adaptive genetic variation structuring beneficial interactions between A. thaliana and the main members of its microbiota.