Understanding the contribution of seed tuber-and soil-borne inocula of Rhizoctonia solani AG 3-PT in causing potato disease epidemics is an important step in implementing effective management strategies for the pathogen. A two-year study was conducted to evaluate the contribution of each source of inoculum using an integrative experimental approach combining field trials and molecular techniques. Two distinct sets of genetically-marked isolates were used as seed tuber-borne and soil-borne inocula in a mark-release-recapture experiment. Disease assessments were done during tuber initiation and at tuber harvest Both inoculuma sources were found to be equally important in causing black scurf disease, whereas soil-borne inocula appeared to be more important for root and stolon infection, and seed-borne inocula contributed more to stem canker. However, seed tuber transmitted genotypes accounted for 60% of the total recovered isolates when genotyped using three PCR-RFLP markers. The changes in population structure of the experimental 1 R. solani population over the course of the growing season and across two growing seasons were investigated using eight microsatellite markers. The populations at different sampling times were somewhat genetically differentiated as indicated by Nei's gene diversity (0.24 -0.27) and the fixation index (F ST ) . The proportion of isolates with genotypes that differed from the inoculants ranged from 13% to 16% in 2013 and 2014, respectively, suggesting the possibility of emergence of new genotypes in the field. Because both soilborne and tuber-borne inocula are critical, it is important to ensure the use of pathogen-free seed tubers to eliminate seed tuber-borne inoculum and the introduction of new genotypes of R. solani for sustainable potato production in South Africa.