Salinity is an edaphic stress and dramatically restricts worldwide crop production. Nanomaterials and plant growth promoting bacteria (PGPBs) are currently used to alleviate of negative effects of various stresses on plant growth and development. In the present study, the protective effects of different levels of zinc oxide nanoparticles (0, 20, and 40 mgl–1) and plant growth promoting bacteria (no bacteria, Bacillus subtilis, Lactobacillus casei, Bacillus pumilus; PGPBs) on DNA damage and cytosine methylation changes were studied in the tomato (Solanum lycopersicum L.) seedling plant under salinity stress (50 mM NaCl). Coupled Restriction Enzyme Digestion-Random Amplification (CRED-RA) and Randomly Amplified Polymorphic DNA (RAPD) approaches were used to analyze changes in cytosine methylation and how genotoxic effects influences estimation and genomic stability. Salinity stress increased the polymorphism rate of RAPD. The relief effect of PGPBs and zinc oxide nanoparticles (ZnO-NPs) also reduced the adverse effects of salinity stress. The genomic template stability value significantly increased across application of PGPB and ZnO-NP treatments, especially, integrating of Lactobacillus casei and 40 mgl–1of ZnO-NPs. DNA hypo-methylation was also observed in all treatments. Taken together, the use of PGPBs and ZnO-NPs nanoparticles induced a positive anti-genotoxic effect. These could be alternative means to reduce genetic impairment in the tomato under salinity stress.