Soybean is an important crop in the Democratic Republic of Congo, a country faced with high levels of war induced malnutrition but its productivity is limited by poor soil fertility coupled with low access to nitrogen mineral fertilizers. Commercial rhizobia strains introduced in 2010 failed to adapt and increase soybeans yields at desired level. We studied the performance of six indigenous rhizobia strains in enhancing soybean productivity compared to two commercial strains USDA110 and SEMIA5019. The study was carried out in the greenhouse and field of Kalambo station of International Institute of Tropical Agriculture (IITA), D. R. Congo during 2016/2017 cropping season. The treatments included: (1) N-, control without inoculation and N-fertilizer; (2) N+, non-inoculated control with 80 kg of N ha −1 ; and inoculated with (3) commercial strain Bradyrhizobium diazoefficiens USDA110; (4) commercial strain Bradyrhizobium elkanii SEMIA5019; (5) local strains Bradyrhizobium japonicum NAC17; (6) NAC22; (7) NAC37, (8) NAC42 (9) NAC 46 and (10) NAC78. Greenhouse and field experiments were laid out as completely randomized design and randomized complete block design respectively. The best inoculation treatments across all experiments were the indigenous strains NAC46 and NAC17 which nodulated equally or better than the commercial strain USDA 110. In the field NAC46 and NAC17 increased soybean grain yield from 2.4 to 3.3 t ha-1 and 3.4 t ha-1 ; indicating the increase of 68.7 and 70.8% respectively, over the commercial strain USDA110. The results demonstrated that indigenous rhizobia NAC46 and NAC17 would thus be the silver bullet to enhanced BNF and soybean yields in South Kivu province of Democratic Republic of Congo.