Isolation from infected watermelon samples has demonstrated the presence of some fungal complex including Fusarium oxysporum, F. solani, Rhizoctonia bataticola, R. solani, Monosporascus cannonballus, Pythium ultimum and P. echinulatum. These fungal species are different in their distribution among the infected plants and areas surveyed. However, F. oxysporum and F. solani are always predominant. These results showed the almost-presence of the two Fusarium disease of watermelon: Fusarium wilt to F. oxysporum f. sp. niveum and the collars and/or root rot caused by F. solani f. sp. cucurbitae which are the primary fungi of sudden wilt. Analysis in main component of isolation frequency of different fungi showed that their association in homogeneous groups seemed not affected by geographic origin and surveyed year.