Spot blotch pathogen Bipolaris sorokiniana of wheat was investigated with threefold objectives: to establish a relationship between morphological and pathological variability of isolates, identify clonal genotype(s) acting as a source for the generation of new variability, and to determine the mechanism of generation of such variability in the pathogen. Isolates were collected from the leaves and seeds of field-grown wheat crop at four different sites in eastern Gangetic plains of India. Eighty-six clonal isolates derived from a single isolate (gray with white patches, Group III), which segregated in an equal proportion of parental and nonparental types, were studied. Morphological characters-i.e., colony morphology, growth rate, and sporulation-were studied along with disease-causing ability of the isolate clones. Clonal isolates were grouped into three categories. Microscopic analysis of nuclei was done to determine the causes of such variability. Morphological variability appeared to be related to the pathological variability. The isolate having epidemic potential appeared different than that acting as the reservoir for variability. The cause of such variability could be attributed either to hyphal fusion and heterokaryosis, nuclear migration and occurrence of multinucleate state, or a combination of these factors. Random Amplified Polymorphic DNA (RAPD) assay suggested that the unique fragments for different groups could be utilized as molecular markers to identify the isolates of specific groups.