The study was undertaken with major objective to differentiate fungal isolates belonging to various species of Bipolaris and Exserohilum infecting various agricultural crops. After routine isolation and purification of more than 35 attempts, 13 isolates were morphologically characterized into 8 species namely, Bipolaris cynodontis (IQBC-1 and DQBC-2), B. holmii (IQBH-1), B. micropus (IQBM-1), B. oryzae (DQBO-1, DQBO-2), B. sorghicola (DQBS-1, DQBS-2), B. tetramera (DQBT-1, DQBT-2), Exserohilum longirostrata (IQEL-1) and E. rostratum (DQER-1 and DQER-2). Molecular characterization of all the isolates using RAPD, ISSR and URP markers also revealed genetic variation. Out of 24 RAPD primers, only 9 (OPA-2, OPA-4, OPA-9, OPB-4, OPB-8, OPC-1, OPC-2, OPC-5 and OPE-5) could amplify the DNA sequence showing good polymorphism. Out of 20 ISSR primers, only 6 (ISSR 1, ISSR 13, ISSR 15, ISSR 17, ISSR 19 and ISSR 20) could show good polymorphism. Out of 13 URPs, only 5 (URP 4R, URP 6R, URP 9F, URP 13R and URP 38F) could amplify with a greater number of bands. In all the three makers, similarity matrix value using Jaccard’s coefficient ranged from 0.149 to 0.548 revealing genetic co-relation among isolates. Combined clustering of RAPD, ISSR and URP data showed relatively low genetic similarity coefficient ranging from 14.92 to 54.76 among isolates which revealed stronger co-relation among isolates. Cluster analysis based on UPGMA provided a clear resolution of relationship among all the 13 isolates belong to 6 Bipolaris and 2 Exserohilum species and confirmed the morphological characterization of the same. Further, molecular markers especially, RAPD, ISSR and URP have revolutionized the genetic analysis of plant pathogens including fungi and their application can greatly help in characterizing related genera and delineation of inter and intra-species complex of fungi.