In this study we developed strain specific Random Amplified Polymorphic DNA molecular markers based on Polymerase Chain Reaction amplification of specific sequence in combination with dilution plating on semi-selective medium to detect and estimate density of propagules of a commercial strains of B. bassiana. Using Random Amplified Polymorphic DNA (RAPD) analysis, the fifteen primers of four Operon series (OPB, OPC, OPE and OPF) were selected for 16 accessions of B. bassiana. All Three Operon series primers (OPB-2, OPB-4 and OPC-4) were highly sensitive and yielded maximum amplification products with all Beauveria bassiana accessions. Analysis of Sixteen accessions of Beauveria bassiana revealed 90.97% of polymorphism. Besides molecular characterization of Beauveria isolates, RAPD markers proved to be very useful in selecting and identifying the specific sequences of B. bassiana for the selective strains which can be developed in future as a more effective bio-control agents.