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Not AvailableQuantitative detection of pathogen DNA load is a crucial aspect in development of disease management strategies and breeding programs. In recent years, there have been several reports where formae speciales specific intergenic spacer (IGS) sequence based markers have been used for quantification of pathogen DNA in different plant and soil samples, through quantitative real-time PCR (qPCR). In the present study, we have utilized an IGS based marker, ISR 52, to detect and quantify Fusarium oxysporum f.sp. ciceris (Foc) DNA, using both conventional PCR and qPCR, in chickpea genotypes which contrast for resistance to Fusarium wilt. Our study reveals that the Foc DNA load was found to be significantly higher in the early wilting genotypes as compared to the wilt resistant genotypes. Late wilting genotype showed a spike in pathogen DNA load in later stage of plant growth. Phenotypic observation of disease progression in combination with qPCR data validated that the pathogen undergoes incubation period before manifestation of symptoms. The above observations provide evidence about the differential dynamics of pathogen build up inside different hosts during different time periods and probable reason for the earliness, lateness and resistance in wilting like traits in these genotypes.Not Availabl