Fusarium oxysporum f. sp. cepae is the causal agent of onion basal rot disease. Onion basal rot disease caused by various Fusarium species is one of the economically important diseases of onion in Egypt. Identification of the prevalent pathogenic species causing onion basal rot disease is essential for designing management strategies, especially to develop resistant cultivars. Fourteen Fusarium isolates were obtained from onion bulbs collected from infected fields of  of four different Governorates (Sharkia, Garbia, Behaira and Monofia) in Egypt. Inoculating onion bulbs (cv. Giza 20) with 14 of Fusarium isolates indicated that the fourteen tested isolates were pathogenic of onion. These isolates were identified as F. oxysporum, F. proliferatum and F. solani based on their morphological and molecular characteristics. As for virulence of each one of the isolates on bulbs and seedlings of onion, F. oxysporum caused severe basal rot and damping-off as a highly virulent species. F. proliferatum attacked onion bulbs while, F. solani caused pre- and post-emergence damping-off over 50%.