A group of twenty faba bean rhizobial isolates was collected from two Egyptian Governorates (Dakahlia and Damitta). The isolates were further morphologically and physiologically characterized to check their growth and symbiotic performance on faba bean plants. According to remarkable lab and pots tests, five rhizobial isolates (Rh 32, Rh 6-A, Rh 3-4, Rh RL3, and Rh 8-A) were selected and subjected to further biochemical and molecular characterizations. Genetic profiling of the five promising rhizobial isolates was conducted using six ISSR-primers. Amplification of bacterial genomic DNA produced a total of 37 genomic loci, 54% of them were polymorphic and 46% were monomorphic. The rate of polymorphism ranged between 25% to 80% with an average of 54%. Clustering pattern analysis of morphological and physiological data grouped the twenty rhizobial isolates in five clusters and the five selected rhizobial isolates were falling close to each other. Clustering analysis of ISSR data grouped the the five rhizobial isolates in four clusters. Analysis based on ISSR data revealed that the lowest genetic distance was 2.00 between Rh 6-A and Rh 3-4 isolates, while the highest genetic distance of 3.61 was between Rh 32 and each of Rh 6-A, Rh 3-4, and Rh RL3 isolates. The greatest similarity measurement was 0.931 between Rh 6-A and Rh 3-4 isolates; while the lowest similarity was 0.745 between Rh 32 and Rh 3-4 isolates. It can concluded that clustering pattern analysis based on molecular data could be used in facilitating the selection of rhizobial isolates that will be promising as a source of genes for biological nitrogen fixation and plant growth-promotion