Collar rot of chilli caused by Sclerotium rolfsii Sacc. is currently occurring in chilli growing areas of Marathwada region in India. The genetic diversity among eight chilli S. rolfsii isolates collected from eight districts covering various geographic areas of Marathwada region of Maharashtra state were analysed using random amplified polymorphic DNA (RAPD) using five random primers. Size of DNA fragments amplified by the five primers ranged from Kb to 10 Kb indicating polymorphism among S. rolfsii isolates. RAPD banding profiles with five different random primers viz., OPA-2, OPA-3, OPA-13, OPA-19 and OPC-5 revealed the existence of genetic variability among the isolates of S. rolfsii and were classified into two main clusters. | Analysis of genetic diversity in Sclerotium rolfsii causing collar rot of chilli by RAPD