Management of Fusarium species associated with seed discolouration of rice was attempted through pathogen derived resistance (PDR). Twenty Fusarium isolates associated with rice varieties Lunishree, Pooja and Sarala were classified into six colour groups on the basis of their colour on Potato Dextrose Agar media. The variability in cultural, molecular characters and virulence were observed among the cultures, associated with the samples of a cultivar drawn from the same seed lot. The vigour index of seedlings of rice cultivar Utkalprabha and Savitri, treated with isolate F14A was considerably more than the untreated control. RAPD-PCR of twelve isolates was done using two primers, AP12h and R-108. The isolate F14A was found to be a fast growing isolate, distinctly different from other isolates and may be suitable for management of this devastating disease by Pathogen Derived Resistance.