The major objective of this study was to investigate biological nitrogen fixation in two main legumes (green gram and common bean) grown in semi-arid southeast Kenya. Nodulation experiments on the two legumes were carried out in the greenhouse of the Botany Department, Kenyatta University with soil samples that had been obtained from Kiboko. Indigenous rhizobia were isolated from the two legumes and screened for the ability to fix nitrogen in comparison with commercially available strains from MIRCEN, UniverSity of Nairobi. The population of indigenous rhizobia specific to the two legumes was determined using the Most Probable Number (MPN) plant infection technique. Results showed that infectivity in common bean was better (80 nodules/plant) than in green gram (18 nodules/plant). Bisection of the nodules showed that 32 % and 77 % of them had an inner pink colour in common bean and green gram, respectively. This is an indication that a majority of the nodules in green gram were effective nitrogen fixers compared to those in common bean. The results of the MPN counts indicated that the number of indigenous rhizobia resident in Kiboko soils, and specific to green gram and common bean were 519-3,780 and 2,037-14,850 rhizobia cells per gram of soil, respectively. Two different isolates of rhizobia for common Bean (C_1S and C_2L) and one for green gram (GG-T), were isolated. Presumptive and authentication tests confirmed these isolates as rhizobia. Greenhouse trials showed thaI isolate C_1S and C_2L was not as effective in nitrogen fixation, as C_2L, and Rhizobium leguminosarum bv. phaseoli strain 446 from MIRCEN although no significant difference in Shoot dry weight was recorded for C_2L and 446. Further, isolate GG-T from green gram was not as effective in nitrogen fixation as the commercial strain Bradyrhizobium sp. strain CB1015.