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Symbiotic nitrogen fixation (SNF) provides much of the N utilized by leguminous plants throughout growth and development. Legumes may simultaneously establish symbiosis with different taxa of microbial symbionts. Yet, the mechanisms used to steer associations toward symbionts that are most propitious across variations in soil types remain mysterious. Here, we demonstrate that GmRj2/Rfg1 is responsible for regulating symbiosis with multiple taxa of soybean symbionts. In our experiments, the GmRj2/Rfg1 SC haplotype favored association with Bradyrhizobia , which is mostly distributed in acid soils, whereas the GmRj2/Rfg1 HH haplotype and knockout mutants of GmRj2/Rfg1 SC associated equally with Bradyrhizobia and Sinorhizobium. Association between GmRj2/Rfg1 and NopP, furthermore, appeared to be involved in symbiont selection. Furthermore, geographic distribution analysis of 1,821 soybean accessions showed that GmRj2/Rfg1 SC haplotypes were enriched in acidic soils where Bradyrhizobia were the dominant symbionts, whereas GmRj2/Rfg1 HH haplotypes were most prevalent in alkaline soils dominated by Sinorhizobium , and neutral soils harbored no apparent predilections toward either haplotype. Taken together, our results suggest that GmRj2/Rfg1 regulates symbiosis with different symbionts and is a strong determinant of soybean adaptability across soil regions. As a consequence, the manipulation of the GmRj2/Rfg1 genotype or application of suitable symbionts according to the haplotype at the GmRj2/Rfg1 locus might be suitable strategies to explore for increasing soybean yield through the management of SNF. [Display omitted] • GmRj2 / Rfg1 determines the taxa of symbionts selected by soybean • Variations in GmRj2/Rfg1 confer better adaptation of soybean in various soil types • Associations between GmRj2/Rfg1 and NopP might be determinant in symbiont selection Li et al. provide new insights into genome-based symbiont selection in soybean, which confers better adaptation to various soil types by regulating the association with different symbionts. This study provides valuable information for soybean breeding programs incorporating beneficial microbes into agriculture management strategies. [ABSTRACT FROM AUTHOR]