Nitraria retusa (Nitrariaceae) is a true xerophyte plant grows in most deserts of Egypt, especially in wadies habitat and dry salt marshes. This study aims to evaluate any possible genetic diversity among samples of Nitraria retusa grown under different habitats using Random Amplified Polymorphic DNA (RAPD) markers, protein electrophoresis and isozyme electrophoresis. For such goal, the ecological aspects of the selected habitats were investigated with the view of finding correlations among these markers and some ecological parameters. Five collected samples of Nitraria retusa were collected from Wadi Hof (sunny and shady), Oyun Musa, Kattamyia and Hammam Faraon. The obtained results showed that differences in the levels of genetic variations detected by the tested markers agree with those observed at the morphological levels. The data obtained from the tested primers resulted in PCR amplified products that differentiate the shady sample of Wadi Hof (with broad leaves) from the other investigated samples. Thus, the results obtained from the present study consider DNA and protein fingerprints for the studied populations.