Analysis of polymorphism among soybean varieties and determination of genetic relationship among soybean varieties differing in Rhizoctonia Aerial Blight (RAB) resistance, using Inter Simple Sequence Repeats (ISSR) marker and Random Amplified Polymorphic DNA (RAPD). In the present investigation carried out 20 ISSR primers amplified 174 markers. Out of them 122 loci were polymorphic 70.11% (6.1±0.52 average), while 52 loci were monomorphic 29.89% (2.6±0.27 average) and RAPD primer amplified 78 loci, out of them 61 loci were polymorphic 78.02% (6.1±0.44 average), while 17 loci were monomorphic 21.78% (1.7±0.44 average). A dendrogram was generated by UPGMA clusters analysis based on Jacquard’s similarity coefficient. Estimated genetic similarity among 18 soybean varieties using 20 ISSR primers, were 0.71 – 0.95. In this study, observed high level of polymorphism because low level of monomorphic band scored this type of markers system.