Genetic variation among the base isolates and monosporidial strains derived from these isolates of Tilletia indica- the causal agent of Karnal bunt (KB) in wheat, was analyzed by morphological, growth behaviors and RAPD-ISSR based molecular polymorphism. Genetic make up of fungal cultures vary among each other. The magnitude of variation in KBPN group is less (narrow genetic base) when compared to the other groups KB3, KB9 and JK (broad genetic base) reflecting that variability is a genetically governed process. The generation of new variation with different growth characteristics is not a generalized feature and is totally dependant on the original genetic make-up of the base isolate generating new monosporidial strains. Thus, it can be concluded that monosporidial strains derived from mono-teliosporic isolate, consists of genetically heterogeneous population. The morphological and genetic variability further suggests that the variation in T. indica strains is predominantly derived through the genetic rearrangements through para sexual means.