The data files contain the genotypic and phenotypic information of a recombinant inbred (RI) population. This population was obtained by crossing the cultivated Glycine max (C08) with the wild type Glycine soja (W05) was adopted from a previous study (Qi et al., 2014). In our previous research (Qi et al., 2014), a core panel of 96 RI lines was re-sequenced at ~1 X depth to generate high-quality single nucleotide polymorphism (SNP) information. An array of high-quality SNPs were grouped into 2,757 bin markers distributed on the 20 chromosomes. A bin map of 2,992.0 cM in the Kosambi mapping function was generated using the bin markers. Biological nitrogen fixation related phenotypes of the RILs were collected in controlled environment as mentioned in materials and methods