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Variation in rhizobia strains isn’t a desirable fact based mainly on the possibility of unexpected results on legume inoculation. In this work, we studied the variability on phenotypic characteristics and genetic stability of rhizobia strains recommended for soybean inoculation. Variants with stable colony morphology were obtained from Bradyrhizobium japonicum strain SEMIA 5080 and from B. elkanii SEMIA 5019. Variants from SEMIA 587 obtained by another author were also used. The variants differed on colony characteristics, nodulation capacity, nitrogen fixation efficiency and competitive ability for nodule formation in two soybean varieties (Jacui 7 and IAS 5). Symbiotic behavior varied according to plant variety. Only the variants 5019 G and 5019 P differed on the isoenzymatic profile. There were differences in antibiotic resistance between variants from two strains. Correlation between symbiotic characteristics and colony morphology or antibiotic resistance wasn’t conclusive. The results indicate that the variability in rhizobia strains might be an important factor to be considered in strain selection and preservation of cultures for inoculant production.