The study was conducted between 2014 and 2016 to monitor the effect of high level concentrations of NaCl on the micropropagation of some grape rootstocks Salt creek, Dog ridge, Richter and Freedom. The genetic analysis of molecular markers was performed using five primers of Inter Simple Sequence Repeat (ISSR). The five ISSR primers produced a total number of amplified bands ranged from 2 to 7 fragments. The highest number of fragments was 7 bands for 17898-B primer. While HB-15 primer generated the lowest number of amplicons (2 bands). The percentage of polymorphism revealed by the different primers ranged from 33.33 to 83.33 % with an average of 54.29 %.  In our analysis we were able to identify and evaluate the grape genetic diversity and to study the phylogenetic relationships between cultivars. Also, the soluble proteins of leaves from four tested grape rootstocks were separated by slab gel electrophoresis into 12 protein bands, but only 2 to 5 bands were found in each cultivar. The peroxidase patterns exhibited a total number of 7 bands in each cultivar three of them were monomorphic bands (Rf = 0.077 – 0.138 – 0.757) in rootstock and under salinity stress. The generic variations detected among closely related genotypes indicate the efficiency of protein and isozyme markers for evaluating and constructing genetic linkage maps and the biochemical genetic diversity of these cultivars.