A combined study of pathogenicity, mycelial compatibility, chemotaxonomic and molecular analyses was conducted to reveal the genetic variability in isolates of Fusarium oxysporum collected fromcotton seedlings in Egypt. The results derived from these techniques were corroborative and suggested a considerable genetic diversity among isolates. However, the extent of diversity differed fromanalysis to another. The virulence of the isolates showed a wide range of variation ranged from 26.6 to 80%. The cluster analysis of mycelial compatibility data indicated no relationship between mycelial compatibility groups and virulence. The high percent of polymorphism at both chemotaxonomic and molecular levels suggested the complex evolution pattern and confirmed the polyphyletic origin of F. oxysporum. In addition, the partial association between the loci generated by one of the used primers and mycelial compatibility groups suggested that somemycelial compatibility groups were clonally derived.