• Biological nitrogen fixation (BNF) is a key process for soybean production in Africa. • The selection of elite African indigenous soybean Bradyrhizobium strains is a feasible strategy. • Eighty-seven isolates were obtained from soybean nodules in Mozambique. • Isolates fit into the Bradyrhizobium (75%) and Agrobacterium-Rhizobium (25%) clades. • Five Bradyrhizobium isolates with outstanding symbiotic performance were obtained.

• Soybean N demand can be fulfilled by biological nitrogen fixation (BNF). • Bradyrhizobium strains from Brazil and USA were tested in Brazil and Mozambique. • Inoculation resulted in grain yield gains of 4–5% in Brazil and 20–29% in Mozambique. • Transference of BNF technologies is feasible, speeding up the production system. • Exotic soybean Bradyrhizobium strains can highly benefit soybean in Mozambique.

Agrobacterium deltaense strain CNPSo 3391 was isolated from a soybean nodule in Mozambique. Its genome size was estimated at 4,926,588 bp.