TWO POT experiments were conducted to investigate the response of five divergent faba bean genotypes namely (NBL- Mar.3, NBL-5, L3, Nubariya-1 and Misr-1) against either drought or salt stresses with split plot design. To achieve this purpose; some morphological characteristics,pigments, carbohydrates, molecular markers, stress tolerance indices and polymorphic information content (PIC) were recorded.   Expose the faba bean genotypes to water and salt stress leads to significant decrease in photosynthetic pigments, total carbohydrates and starch. A significant increase in total soluble sugar content with increasing the salt and water stress levels were detected in all genotypes. Tolerant genotypes (NBL- Mar.3 and NBL-5) have high chlorophyll, carbohydrates and starch content than  sensitive genotypes (Nubariya-1 and Misr-1). Seed yield /plant presence wide range of differences among all genotypes in each of the two abiotic stresses in focus. This reflects a fluctuation response in each of the eleven tolerance indices. NBL-5 considered as the highest drought tolerant genotype while Misr-1 is the most sensitive one. Similar conclusion is true for NBL- Mar.3 as a best tolerant genotype under salinity experiment conditions while, Nubariya-1 and Misr-1 were the most sensitive one.  The highest water deficit newly bred tolerant genotype (NBL-5) discriminated by either two positive specific markers at amplified fragments (AF) (45 and 61) or three negative amplicons at AF (30, 32 and 33). The salt tolerant genotype (NBL- Mar.3) own ten of the unique amplicons out of the 40 total number of specific markers (TSM) which including either the presence or absence of a given band. These specific markers could be successfully used as marker assisted selection (MAS) for the best genotypes utilizing in faba bean breeding programs.   The dendrogram results classified the five faba bean genotypes under consideration into two main clusters. The first cluster comprised the two newly bred lines (NBL- Mar.3 and NBL-5) which shared in one parent of their ancestors and this could confirm the highest similarity value between them.