Nine faba bean lines were screened for resistance to chocolate spot, caused by Botrytis fabae. in vivo, using the detached leaf technique as well as under growth-chamber controlled conditions, and under field conditions during two seasons, i.e., 2006/2007 and 2007/2008, at Maryout Experimental Station. There were a significant correlation between disease score index and diameter of lesions, using detached leaf assay. The disease progressed gradually by increasing the time of incubation. Genotype Aquadulce recorded the lowest lesion diameter during the tested time with average of 0.18 mm followed by line L8 with 0.25 mm. Genotypes showed different degrees of disease severity using detached leaf assay. Aquadulce and L8 were resistant genotypes 6 days after inoculation Under growth chamber-controlled conditions, significant differences were detected among the nine faba bean genotypes against chocolate spot according to their Mass Disease Index (MDI). Most genotypes were susceptible (s) to moderately susceptible (MS), and the Spain genotype Aquadulce was moderately resistant (MR) to chocolate spot. Under field conditions, during the two seasons, 2006-2007 and 2007-2008, the tested genotypes showed different degrees of reaction to chocolate spot with ranged from resistant to moderately susceptible according to their MDI. The check variety Giza 461 and the newly bred line NBL2 scored the lowest MDI (11.1) and classified as resistant, while the other genotypes were classified as moderately resistant to chocolate spot. Aquadulce genotype recorded the highest values for 100/seed weight (88.7 g.). Line NBL3 recorded the highest values of number of pods /plant while line L8 was the lowest one. Among all genotypes, Line NBL4 exhibited the highest means for number of seeds/ pod (4.8) while line L3 recorded the maximum value for seed yield/plant (69.54 g). DNA analysis of the tested genotype) showed that there is a specific molecular marker limited with disease resistance by using the primer 841. ISSR - PCR of eight primers discriminated the genotypes tested and the SPSS dendrogram classified them into two main clusters.