This field experiment was conducted with the aim of studying the chemical, anatomical and molecular indicators of wheat cultivars under irrigation with levels of salinity stress. The results of the statistical analysis showed a significant difference in the effect of the high salinity concentration of irrigation water on the chemical traits such as the proline content and protein, the lowest average was (10.37 and 25.96)% respectively. It also affected the anatomical traits represented by the number of the stomatal of the upper and lower surfaces of the leaf with the lowest average of (8.11, 6.22) stomata mm-2 respectively, while the cultivar differed significantly, as the Russian cultivar showed superiority in the proline content and protein, while the Mawada cultivar was superior in the relative water content and stomata density on the upper and lower surfaces. The results of the molecular analysis by RAPD-PCR technology showed that the primer UBC1 gave the highest number of band, which amounted to 58 total band, and the primer OPD-02 scored 49 relevance band, including one unique band, while the primer OPS-19 showed the lowest band number, reached 30, including a unique band. It constitutes a genetic fingerprint for these two primers.