This study aimed to detect variations between four faba bean cultivars by using hybridization between minor and equina types. In addition, studying the detected variations on molecular markers level using ISSR, and determine the genetic similarity between faba bean plants and its parasitic weed Orobanche crenata. Five different ISSR primers were used, and general results showed that the total amplified fragments (TAF) induced in the three crosses using all primers were 270 bands (with an average 18 per primer) which distributed as 195 polymorphic bands (PB), 75 unique bands (UB), and finally there was not any monomorphic band (MB). The molecular similarity between faba bean host and Orobanche parasite may indicate some kind of complementary genes system controlling interaction of the host and the parasite.