Fusarium oxysporum f.sp zingiberi (FOZ) is one of the most important pathogens of ginger. Infection by FOZ is difficult to control since thefungus can grow saprophytically in the absence of the host. Conventional breeding methods for selection of disease resistant varieties are lengthy and cumbersome. Bioassays in vitro and in vivo were performed to assess different degrees of sensitivity of eight varieties of ginger. Random Amplified Polymorphic DNA (RAPD) analysis of genomes from the eight ginger varieties, using 15 different primers was performed to verify the DNA polymorphism. Five primers showed no polymorphic profiles, eight primers gave polymorphic bands and two primers produced highly specific polymorphic bands allowing us to obtain RAPD profiles typical of the most resistant or susceptible varieties. The RAPD pattern is correlated to the sensitivities of the ginger varieties to the pathogen as observed in the bioassays. Cloning and sequencing the most interesting polymorphic DNA fragment revealed 60% homology with putative reverse transcriptase in chickpea and Lotus plane tree, which was linked with resistance. This is the first report of a RAPD marker linkedto resistance against fusarium yellows in ginger.