Abstract: The effect of MS and water agar medium, containing NaCl and sucrose on germination percentage, seedling growth, chlorophyll content, acid phosphates activity and soluble proteins were studied in different cultivars of Lycopersicon esculentum Mill. (Cv. Isfahani, Shirazy, Khozestani and Khorasani). Seeds were germinated under various mediums, MS with and without sucrose, water agar with and without sucrose with different concentration of NaCl (0, 40, 80, 120 and 160 mM). Increasing of salinity decreased the germination percentage and seedling dry weight. The highest germination percentage was found in Cv. Isfahani and the lowest in Cv. Shirazy. Chlorophyll content (Chl a, Chl b and total Chl) were decreased with increasing of salinity in both Cv. Isfahani and Shirazy. In Cv. Shirazy. Acid phosphates (Apase) activity was decreased in stem-leaf while it was increased in roots. Soluble protein was changed in different salt concentration. Enzyme activity was decreased in stem-leaf in Cv. Shirazy but was increased in Cv. Isfahani. Soluble proteins in roots of both Cv. showed variation. Finally, Water Agar (WA) medium in comparison with MS medium resulted in higher tomato seed germination in different NaCl concentration.