We explored the genetic basis of SNF-related traits through GWAS and identified 40 candidate genes. This study provides fundamental insights into SNF-related traits and will accelerate efforts for SNF breeding. Symbiotic nitrogen fixation (SNF) increases sustainability by supplying biological nitrogen for crops to enhance yields without damaging the ecosystem. A better understanding of this complex biological process is critical for addressing the triple challenges of food security, environmental degradation, and climate change. Soybean plants, the most important legume worldwide, can form a mutualistic interaction with specialized soil bacteria, bradyrhizobia, to fix atmospheric nitrogen. Here we report a comprehensive genome-wide association study of 11 SNF-related traits using 79K GBS-derived SNPs in 297 African soybeans. We identified 25 QTL regions encompassing 40 putative candidate genes for SNF-related traits including 20 genes with no prior known role in SNF. A line with a large deletion (164 kb), encompassing a QTL region containing a strong candidate gene (CASTOR), exhibited a marked decrease in SNF. This study performed on African soybean lines provides fundamental insights into SNF-related traits and yielded a rich catalog of candidate genes for SNF-related traits that might accelerate future efforts aimed at sustainable agriculture.