The legume-rhizobia symbiosis is considered one of the most important plant-microbe interactions in the biosphere. The relevance of this symbiosis lies in the possibility of replenishing the soil with fixed-nitrogen, action that can contribute to the development of sustainable agriculture and reduce the use of fertilizers. Understanding of the molecular events underlying the symbiosis is key to enhance the nitrogen-fixation efficiency. Medicago truncatula has been used as model plant for studying plant-microbe interaction in legumes due to the several resources available (genome sequence, gene expression data and mutant collections). The advent of new resources in molecular biology, has made possible to obtain new data to elucidate the underlying molecular mechanisms in different biological processes. Genome-wide association studies (GWAS) has been an important tool that combines newer resources available in molecular biology (next generation sequencing), to produce genome-wide single nucleotide polymorphisms SNPs, and complex statistical analysis to search for the genetic architecture of complex traits. A GWAS analysis was performed to identify the genetic basis of the mutualism variation in M. truncatula – Ensifer spp. complex. Based on Batstone, et al. 2021, two Ensifer spp. strains were selected and used as inoculum source in a subset of 149 accessions of the M. truncatula hapmap population to identify genes associated with the partner choice selection of M. truncatula for a specific Ensifer spp. strain