Twenty three fatty acid profiles were qualitatively and quantitatively determined by using fatty acid methyl esterification (FAME) to differentiate between three isolates of Fusarium oxysporum f.sp. vasinfectum, the cotton wilt pathogen, and seven isolates of Fusarium oxysporum from other hosts. Cluster analysis by the unweighted group method with arithmetic mean (UPGMA) demonstrated that although qualitative profiles were simpler than the quantitative ones, they were more useful in differentiation between Fusarium oxysporum f. sp. vasinfecolates and the other isolates of Fusarium oxysporum.