In the present investigation biochemical characterization of pearl millet genotypes was carried at pre and post-infection stage while molecular characterization was carried out at seedling stage without infection.These results suggested that SOD, PPO and ß-1,3-glucanase enzymes can work as biochemical markers and ISSR as a molecular marker may be used for large scale screening of germplasm for disease reaction trait. Overall pooled analysis of isozymes, protein profiling, RAPD and ISSR data analyzed through Jaccard's similarity coefficient and subject to a dendrogram construction showed two distinct cluster of resistant and susceptible genotypes.