ABSTRACT: Gene polymorphism can be used to study the genetic diversity of fungal populations, as well as the relationship between different fungal isolates and strains. Our goal in this study is to use random amplified polymorphic DNA (RAPD) and protein analyses to characterize 10 Fusarium isolates were obtained from five different Egyptian sites. The results revealed that the polymorphism percentage ranged from 62.5 to 91.7, with an average of 81.1 per primer. In terms of polymorphic information content (PIC), RAPD primers had an average of 0.35 and a range of 0.3 to 0.41. Resolving power (RP) values varied from 1.6 and 6.6 with an average of 3.6 per primer. The primer OPB-01 produced the highest effective multiplex ratio (EMR) value (10.1), whilst the primer P-005 produced the lowest value (3.12), with an average value of 6.39 per primer. The range of marker index (MI) values was 0.72 to 4.14, with an average of 1.96 per primer. For primers P-006 and OPB-01, the diversity index (DI) values per polymorphic band ranged from 0.08 to 0.38, respectively. RAPD markers yielded genetic similarity values ranging from 0.62 to 0.92, with an average of 0.75. The ten isolates were divided into two major clusters. Isolates R1, R8, R10, R9, R3, and R2 were placed in the first one, while isolates R5, R6, R4, and R7 were located in the second one. Isolates R8 and R10 had the highest similarity index (0.92). The isolates R4 and R7, on the other hand, had the lowest similarity index score (0.75). The dendrogram of protein banding patterns contains the isolate R7 on one cluster with44% similarity. While the remaining isolates (R1, R2, R4, and R10) are found in the second cluster. The second cluster split into two branches with a commonality of 54%. The isolates R3 and R8 were gathered as a single branch on the first branch. The isolates R1, R4, R2, and R10 were all part of the first subbranch. The isolates R5, R6, and R9 were all part of the second subbranch. Indicators of similarity varied from 44% to 96%. The wide genetic variation among Fof isolates is a major challenge for the development of effective disease control strategies. Therefore, our study using protein and RAPD markers for assessing the genetic diversity of F. oxysporum f. sp. frageria isolates can be a useful tool for understanding the relationship among different isolates as a base for investigating the relationship between genetic diversity and pathogenicity to develop a suitable program against different F. oxysporum f. sp. frageria pathotypes in the future.