Limited information is available on reduced cowpea (Vigna unguiculata L. Walp.) and green gram (Vigna radiata L.Wilczek.) yields in Kenya. Declining soil fertility and absence or presence of ineffective indigenous rhizobia in soils are assumptions that have been formulated but still require to be demonstrated. In this study, soils were collected from legume growing areas of Western (Bungoma), Nyanza (Bondo), Eastern (Isiolo), Central (Meru) and Coast (Kilifi) provinces in Kenya to assess indigenous rhizobia in soils nodulating cowpea and green gram under greenhouse conditions. Our results showed that highest nodule fresh weights of 4.63 and 3.32 g plant_1 for cowpea and green gram were observed in one soil from Isiolo and another from Kilifi, respectively, suggesting the presence of significant infective indigenous strains in both soils. On the other hand, the lowest nodule fresh weights of 2.17 and 0.72 g plant_1 were observed in one soil from Bungoma for cowpea and green gram, respectively. Symbiotic nitrogen (N) fixation by cowpea and green gram was highest in Kilifi soil with values of 98% and 97%, respectively. A second greenhouse experiment was undertaken to evaluate the performance of commercial rhizobial inoculants with both legumes in Chonyi soil (also from Coast province) containing significant indigenous rhizobia [>13.5_103 Colony Forming Units (CFU) g_1]. Rhizobial inoculation did not significantly (P < 0.05) affect nodulation, biomass yield and shoot N content in cowpea and green gram compared with controls. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) of the 16S-23S rDNA intergenic spacer (IGS) region analysis of nodules revealed six groups of which only IGS Group IV corresponded with those from commercial inoculants applied, indicating a lower competitiveness of inoculated strains. In cowpea, IGS III was dominant in nodules of plants inoculated with Biofix and Rizoliq commercial inoculants, and the uninoculated c