Limited information is available on reduced cowpea and green gram yields in Kenya. Declining soil fertility or presence of ineffective indigenous rhizobia? In regards to this, soils were collected from Western province (Bondo, Bungoma) to Eastern (Isiolo), Central (Meru) and at the Coast (Kilifi) to trap indigenous rhizobia nodulating both legumes under greenhouse condition. Highest nodule fresh weights of 4.63 and 3.32 g plant-1 for cowpea and green gram were observed in soil from Isiolo site A and Kilifi site A respectively suggesting significant populations of indigenous strains in such soils. Lowest nodule fresh weights of 2.17 and 0.72 g plant-1 were observed in soil from Bungoma site B for cowpea and green gram respectively. Genetic diversity of indigenous strains nodulating both legumes was assayed using PCR-RFLP of the 16S-23S rDNA IGS and 19 IGS groups were identified with I and II predominating for both legumes. A second greenhouse experiment was set up to evaluate if commercial inoculants significantly improve cowpea and green gram yields in soils with significant populations of native rhizobia. Rhizobial inoculation did not significantly (p<0.05) affect nodulation and biomass yield in cowpea. In green gram, the highest and lowest nodule fresh weights were observed in green gram peat and Rizoliq treatments (2.99 and 1.63 g plant-1) respectively and the highest and lowest biomass yields were observed in Mineral N and Rizoliq treatments (12.41 and 11.85 g plant-1) respectively. PCR-RFLP analysis revealed 6 IGS groups none of which corresponded with those from commercial inoculants applied, indicating a lower competitiveness of inoculated strains. IGS group III was predominant in nodules from both legumes and present in all treatments. Our results suggest that the systematic inoculation of both cowpea and green gram with commercial inoculants to improve yields is not really justified, native strains performing better than inoculated strains. (Texte intégral)