Bakanae of rice caused by Fusarium fujikuroi has become an important disease in major rice production regions worldwide. Twenty-nine isolates of F. fujikuroiwere differentiated based on produced pigments, gibberellic acid (GA₃), molecular characteristics and correlated with bakanae disease symptomsof rice seedling. All isolates of F. fujikuroi produced pigments except six isolates. Also, all isolates differed in the production of gibberellic acid. The isolate FI 12 was the highest produced for GA3 and disease severity index. Molecular analysis showed that nine ISJ primers produced a total of 809 amplified bands. Current results indicated that the Fusarium isolates were clustered largely based on location and/or severity of isolates and level of GA3 production. The molecular results obtained proved the existence of high levels of genetic variation and high-resolution power of ISJ marker in detecting Fusarium molecular diversity. The differential behavior of bakanae pathogen in resistant and susceptible rice genotypes during infection was studied. Under greenhouse condition, Giza 177 was highly susceptible to rice genotypes while Giza 179 and Giza 178 were moderately resistant. Biochemical changes such as antioxidant enzymes and hydrogen peroxide (H₂O₂)was observed in rice seedling after 7, 15 and 21 days from inoculation. Enzymes activities were increased in Giza 179 and Giza 178 genotypes, but in H₂O₂ content was decreasing. Under field conditions, all genotypes showed increased chlorophyll content, number of tillers/hills and means of panicle length/10 healthy plants compared with infected plants. Giza 179 showed the highest grain yield.