Karnal bunt of wheat caused by Tilletia indica (syn. Neovossia indica) is an important disease in northwestern plains of India. Besides India, the disease is also known to occur in several tropical and sub tropical areas of the world including Nepal, Pakistan, Mexico, North-Western Europe and USA. Fungal genomic DNA of ten T. indica isolates of North Western Plain Zone, was isolated from fresh mycelia by using the CTAB method. Inter simple sequence repeat (ISSR) primers were used to study the genetic variation among T. indica isolates. A total of 192 bands were observed with 28 polymorphic primers (ISSR) used. Pair wise similarity index values ranged from 0.61 to 0.96 for all isolates. Isolates were grouped in different clusters according to their similiarity. The cluster analysis further validated with PCA (principal component analysis) also. Thus ISSR primers showed genetic variation among ten T. indica isolates belonged to north western plains of India. In an earlier study, genetic variation among Tilletia indica isolates was also observed with RAPD by using oligonucleotide primers. Head scab or Fusarium head blight (FHB) is a destructive disease of wheat almost worldwide. Disease is of minor importance in India but due to global climate change, extensive survey is being carried out every year in disease prone areas (lower, mid and high Hills of Himachal Pradesh, foot hills of Punjab, Wellington-Nilgiri hills of Tamil Nadu) since 2000. Fusarium graminearum was found most dominating spp. causing FHB in India. Pathogenic variation was observed on a set of wheat varieties among Fusarium spp./isolates. Genetic variation among F. graminearum isolates has been studied with RAPD primers and microsatellite markers. The study has shown that there is considerable genetic variability among Fusarium spp./isolates causing FHB in India.