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Forty-eight isolates of FOC collected from different chickpea growing regions in India were evaluated for genetic variations using amplified fragment length polymorphism (AFLP). Out of 48 isolates, 41 werefound pathogenic and seven non-pathogenic. Pathogenic isolates differ in their virulence however; there was no apparent correlation between geographical origin and virulence of the isolates. The genetic variation was evaluated by the AFLP analysis. A total 339 fragments were scored following selective amplification with five EcoR1 and Mse1 primer combinations E-TC/M-CAT, E-TC/M-CAC, EAC/ M-CAG, E-TA/MCAG, E-TA/M-CAG, out of which 331 fragments were polymorphic. UPGMA cluster analysis and principle coordinate analysis distinctly classified 48 isolates into two major groups; pathogenic and non-pathogenic. The pathogenic isolates could be further clustered into six majorgroups at 0.77 genetic similarities. Region specific grouping was observed with in few isolates. The results of the present study provide evidence of the high discriminatory power of AFLP analysis,suggesting the applicability of this method to the molecular characterization of Fusarium oxysporum f.sp. ciceris.