Field and laboratory experiments were carried out at the Farm of El-Gemmeza Agricultural Research Station, Gharbia Governorate and Seed Technology Research Department, ARC, Egypt, during 2010/2011and 2011/2012 seasons to identify and discriminate ten faba bean genotypes using morphological characters and molecular marker. The results revealed that some morphological characters such as pinnul shape, lines density of flag flower, pod color at maturity, testa shape and color were useful to identify some genotypes from each other, while they were not enough for identifying other genotypes. By using Inter-simple sequence repeat (ISSR-PCR) technique, it was possible to determine the genetic diversity and relationships of the ten faba bean genotypes included in this study. A total of 71 amplified bands were generated with five ISSR primers, of which 59 (83.1%) were polymorphic which represent a relatively high polymorphism level. These results are important in protecting of plant breeders rights and at releasing these genotypes as a new varieties.