I this study, 22 genotype and lines of grass pea under cold climate of Maragheh were evaluated to fine their genetic diversity for water stress tolerance and low ODAP with some physiological, biochemical and molecular techniques. 19 EST-SSR markers were selected for genetic diversity. The results showed that there was polymorphism in all markers but the highest amount of polymorphism was observed in locus S33. The low rate of polymorphism may be due to the genetic structure of EST-SSR primers, which have a low tendency to polymorphism due to the preservation of larger DNA sequences in the transcription region. High number of alleles in each locus can be due to the high difference and variety in the number of genotypes of different geographical origins. The results of expression of genes related to the cysteine synthase enzyme showed that this gene was higher in mature leaves and in high-yield genotypes than early genotypes and low neurotoxin content. Lines number 3, 15, 4, 17 and 18 produced more abscisic acid and had more content of Glycine betaine and Proline thus, they have been able to protect their cells from drought stress injuries. Also, these lines have low levels of antioxidant enzyme activity, which indicates the stability of their biochemical activity level. Mentioned lines had low levels of neurotoxins with high biological performance compared to other lines.