Rhizobia as useful soil bacteria can coexist with legume and fix nitrogen. Nanoparticles (NPs) are now widely used in various branches of science and silver (Ag) and zinc oxide (ZnO) NPs are the most widely used in this area. These particles finally enter in aquatic and terrestrial environments and probably have harmful effects on living organisms and environments. The aim of this study was to evaluate the effect of silver and ZnO NPs on Sinorhizobium meliloti and alfalfa symbiosis. S. meliloti bacteria were isolated from the alfalfa root nodules. Minimum inhibitory concentrations (MIC) of NPs were determined by agar dilution method. The effects of NPs on nodulation were studied by plant infection test in Jensen-nitrogen free agar medium. The gene expression of nitrogen fixation (nif gene) was evaluated in the presence of NPs by Real Time PCR. It was found that in the presence of NPs, the total length of treated plants and the number of nodules were decreased by increasing the concentration of NPs (1.25 to 10 μg/ml of AgNPs and 12.5 to 100 mg/ml of ZnO NPs) compared to the control plants (p ≤ 0.05). nif gene expression was decreased in the presence of sub MIC concentration of NPs.