Seed samples of 7 flax cultivars (Giza-8, Giza-7,Giza-6,Giza-5,Sakha-1, Sakha-2 and Marline), were screened for the associated seed-borne fungi,15 fungal species were isolated belonging to 11 genera .The isolated fungi were Aspergillus niger, Aspergillus flavus , Aspergillus ochraceous, Alternaria altrenata, Cladosporium sp.,Chatomium sp., Drechslera sp., Epicoccum sp., Fusarium oxysporum, Fusarium solani, Fusarium moniliforme,Penicillium sp., Stemphyllium sp.,Phoma sp., Trichoderma sp. The genus Aspergillus recorded the highest percentage of seed colonization between the seven tested flax cultivars, ranged from (2-20%). Pathogenicity test for 14 isolates of F. oxysporum were studied for the levels of pathogenicity on seven flax cultivars under greenhouse conditions.Percentage of infection was used as a criteria to evaluate the pathogenicity of  F. oxysporum isolates  some of the tested isolates i.e. isolate no. 8 showed (85.0%), followed by isolate no.13 at 73.33% on flax cultivar (Giza-8). Moreover, cluster analysis was a reliable method to differentiate between 14 isolates belonging to the closely related F. oxysporum. Similarity coefficient matrix of F.oxysporum ,isolates ,involved in flax seedling damping-off  showed a few  significant correlations between the tested isolates of F. oxysporum,  based on their pathogenicity on 7 flax cultivars.