Method for molecular analysis of genetic diversity in Fusarium oxysporum f. sp. ciceris by rep-PCR. The method comprises (i) obtaining DNA fingerprints of F. oxysporum f. sp. ciceris by rep-PCR and (ii) compare said fingerprints with a set of DNA fingerprints obtained by rep-PCR representative of different isolates and races of F. oxysporum f. sp. ciceris, in which obtaining said DNA fingerprints of F. oxysporum f. sp. Ciceris is made by contacting DNA of said fungus with a reaction mixture for the enzymatic amplification of DNA, which comprises a pair of specific primers for the enzymatic amplification of repetitive elements of the genomic DNA of said fungus. Applicable in the molecular analysis of the genetic diversity of breeds of F. oxysporum f. sp. Ciceris
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