The aim of this study was to investigate the regional dependant genetic variation among different pathogenic Fusarium solani isolates and a link to persistence cause of shisham dieback in various agro ecological zones. A total of 23 pathogenic representative isolates of Fusarium solani, collected from various agro ecological zones were subjected to analysis of genetic variability in terms of DNA polymorphism using RAPD-PCR. Results were obtained with the help of 10 randomly amplified polymorphic DNA markers (OPA1-OPA10) to test genetic variability in F. solani isolates. A total of 238 amplified products generated with the primers and 23 isolates of F. solani. The pattern of genetic variability in the isolate was also supported by the analysis of the similarity indices and UPGMA dendrogram. Twenty three isolates of F. solani recovered from different areas showed a significant genetic variation durning RAPD analysis. It seems that the genetic variability among fungal isolates is regional dependent and reason of persistent cause of shisham dieback in Punjab, Pakistan. Current findings showed the variation among pathogenic isolates of F. solani and ravealed that persistent cause of shisham dieback is due to F. solani complex in different shisham growing regions in province Punjab, Pakistan.