In the current study, we recovered sixteen bradyrhizobial isolates from root nodules of two soybean genotypes (JS 335 and PK 472) grown in two distinct agro-climatic conditions (Bundi and Udaipur) of Rajasthan, India. Symbiotic effectiveness of these isolates was evaluated under greenhouse conditions. On the basis of statistical analysis of data (ANOVA followed by LSD P ⩽ 0.05), four effective isolates namely BJ335-1, BPK-3, BPK-5 and UJ335-1 were screened out from the greenhouse experiment. The compatibility to three soybean genotypes, and the competitive ability with other field population of rhizobia, of these four isolates was further determined by conducting field trial. Results demonstrated significant variation in the symbiotic potential of tested isolates with respect to different soybean genotypes. Response of soybean genotype JS 335 towards inoculation was relatively better suggesting its suitability in the Haroti region of Rajasthan. Moreover, BJ 335-1 and BPK-3 isolates were found to be highly efficient as they significantly improved the nodulation, plant growth and seed yield. Possible factors responsible for variable response of bradyrhizobial isolates towards inoculation in three soybean genotypes are discussed. Further, the inoculants production of effective isolates at large scale and their multilocational trials are required to check their suitability for the other agro-climatic conditions.