This study used seven inter-simple sequence repeat (ISSR) markers to characterize 55 R. solani isolates in order to establish their genetic diversity. The isolates were from five common bean growing agro-ecological zones of Uganda; the Southwest highlands (SW), Lake Victoria crescent and Mbale farmlands (LVC), Teso farming system (TFS), the Northern mixed farmlands (N) and the Western highlands and Semliki flats (W). DNA was extracted from 7-day old R. solani isolates growing on potato dextrose agar and amplified using PCR. Molecular analysis based on the ISSR fingerprints established moderate genetic diversity (mean = 0.389 ± 0.022). In addition, a high degree of intraspecific variation was observed by cluster analysis which generated a dendrogram with 5 highly reliable clusters (p ≥ 0.95) whose composition was independent of agro-ecological zones. Further evidence of intraspecific variation was provided by analysis of molecular variance which ascribed all the observed variation to genetic differences within the isolates. Isolates from SW, W, TFS and N had significant standardized index of association values indicative of clonal reproduction while isolates from LVC did not have significant values whence were sexual. The genetic diversity revealed by our study means that screening common bean germplasm for sources of resistance to R. solani should be done using diverse pathotypes and secondly, the breeders should pyramid many disease resistance genes in elite cultivars to provide durable resistance against R. solani.