This investigation was conducted at the laboratory of Seed Technology Research Department at Sakha Agric. Res. Station ARC, Egypt, during the year of 2016-2017, to study the effect of salinity of four sea water levels i.e. 0, 4, 6 and 8ML^-1 mixed with distillated water which was used as the evaluation included a control seed germination, shoot length, root length, seedling fresh and dry weight of all 16 genotype varieties. The experimental design was factorial completely randomize arrangement Excluded in a design with three replicates. Seeds were sowed in patri-dishes. The effect of seawater concentrations varied significantly where the germination percentage, shoot length, root length, fresh weight and dry weight decreased with the increasing of the seawater concentrations from 0 to 8ML^-1. The maximum germination percentage was found with fahl genotype (mono cut type) and for Sakha 4 (mult- cut type). Among the 64 treatments combinations the lowest germination percentage was found in population 46 and differed, in fresh weight for the seedling which ranged between 185.83 and 50.83 (mg) for Fahl and Sakha4, respectively while genotype Helaly gave 237.50(mg). The highest germination percentage was obtained for Serw 1, Fahl, Sakha4 and Sakha 96 genotypes, respectively. On the other hand, the lowest germination percentage under the highest level was Sakha comp 2000. ISSR (Inter Simple Sequence Repeat) and Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) analysis were utilized in this study to evaluate at molecular level the differences between levels of water salinity stress of   Egyptian clover. Five primers of ISSR generate highly genetic variation for resistance, moderate and sensitive. Clover genotypes resulting in salinity stress. 72, 68, 62, 31, and 25% of genetic similarity were reflected for third, fifth, fourth, second and first ISSR primers. Common important protein fraction with 54 KDa was expressed in all resistance, moderate and sensitive as well Egyptian clover which refers to its importance role in salinity metabolism cycle. Varied protein interactions were distinguished clearly and showed different responses or reaction for salinity level.