Ninteen species belonging to genus Ficus were obtained from three Egyptian gardens to study the information derived from ISSR fingerprinting, and to estimate the level of polymorphism and genetic similarity. Five ISSR primers were used to estimate the level of polymorphism among the different species. This study indicates that, the total number of bands detected by the different ISSR primers was 229 all of them were polymorphic, representing a level of polymorphism of 100% and an average number of 46 polymorphic bands per primer. The ISSR analysis revealed the highest genetic similarity (85%) between F. afzelii and F. benghalensis, while the lowest genetic similarity (58%) was observed between F. carica and F. sycomorus. The obtained results clearly revealed a high level of similarity among the investigated Ficus species, ensuring the highest degree of homology and the narrow genetic background of these species. The two studied taxa of subgenus Ficus, viz., F. carica and F. deltoidea were widely separated and showed relations with the taxa of subgenus Urostigma. Also, the three studied taxa of subgenus Sycomorus possessed relations with members of subgenus Urostigma.