Fusarium oxysporum is common in soils of Egypt. Wilt is one of the major factors for low productivity of cucumber (Cucumis sativus L.). Four Fusarium isolates were isolated from different soils, identified and screened for pathogenicity and genetic variation using RAPD (Random Amplification of Polymorphic DNA) markers. Disease severity and variations in the symptoms were recorded for all isolates. F. oxysporum isolates have no typical RAPD profiles and all the four isolates showed a close similarity after the development of a phylogenetic tree. The RAPD-PCR (RAPD-Polymerase chain reaction) may be valuable in monitoring populations and characterization of different pathotypes of F. oxysporum. Clustering analysis based on RAPD fingerprint data revealed two distinct groups within F. oxysporum, which often correspond to the origin of the isolate.