During the last several years, the world as well as Croatia, have been affected by the extreme weather events as a result of climate change. Such changes have immense effect on human and natural ecosystems, more precisely on agriculture, which is directly dependant on changes concerning the climate. It has become of crucial importance to follow the inputs of sustainable agriculture and reduce the negative consequences on the environment. One of such sustainable processes in the nature is biological nitrogen fixation, where rhizobia form a symbiotic relationship with most legumes, which results in converting the atmospheric nitrogen to organic forms which can be used by plants. Futhermore, the selection of rhizobial strains that have demonstrated effectiveness even in the unfavourable conditions would enable the further exploatation of this natural process even in the areas affected by extreme environmental conditions. The aim of this study was to isolate and identify rhizobia that were obtained from flooded areas of županjska Posavina. Molecular methods used for the genetic characterization of isolated bacteria were 16S rDNA PCR – RFLP, RAPD and rep – PCR methods. The results based on 16S rDNA PCR – RFLP method showed that majority of the isolates could be regarded as Bradyrhizobium japonicum. RAPD and rep – PCR methods showed a considerable level of genetic diversity among isolated strains, but also proved that the greatest similarity between the strains are strains isolated from Rajevo Selo.