The cultivated area with faba bean in Egypt was decreasing therefore, it is necessary to find ways to increase the productivity of feddan so, breeding programs with estimating of genetic variation are important to obtain the best results. In present study, we have evaluated eighteen faba bean genotypes for earliness, yield and yield attributes and assessed genetic diversity using protein, ISSR and SCoT marker. High significant differences were observed between genotypes for earliness traits, yield and its attributes in both seasons. On the other side, the correlation coefficients were significant between number of pods/nod and each of number of seeds/pod, number of seeds/plant, 100-seed weight and seed weight/plant in both seasons, respectively. Seven Inter simple sequence repeat (ISSR) and six start codon targeted (SCoT) primers had success to produce polymorphic bands that were effective for studying the genetic variation between the studied genotypes. Out of 149 clear bands detected, 57 for ISSR and 76 for SCoT were polymorphic with 86.2 and 92.8 polymorphism percentage, respectively. SCoT markers provided more discriminating data. Cluster analysis based on collected data of protein, ISSR and SCoT succeeded in detection of genetic variety and heterogeneity within the genotypes.so, Crosses between different genotypes based on Cluster analysis could lead to the development of effective breeding materials. Therefore, we recommend using the obtained divergence result when planning crosses between the studied genotypes in faba bean breeding program.