Rhizoctonia solani AG 3-PT is an important potato pathogen causing significant yield and
quality losses in potato production globally. However, little is known about the levels of
genetic diversity and population structure of this pathogen in South Africa. A total of 114 R.
solani AG 3-PT isolates collected from four geographic regions were analyzed for genetic
diversity and structure using eight microsatellite loci. Microsatellite analysis found high intrapopulation
genetic diversity, population differentiation and evidence of recombination. A total of 78 multilocus genotypes (MLGs) were identified with few MLGs shared among
populations. Low levels of clonality (13-39 %) and high levels of population differentiation
were observed among populations. Most of the loci were in Hardy-Weinberg equilibrium and
all four field populations showed evidence of a mixed reproductive mode of both clonality
and recombination. The PCoA clustering method revealed genetically distinct geographic
populations of R. solani AG 3-PT in South Africa. This study showed that populations of R.
solani AG 3-PT in South Africa are genetically differentiated and disease management
strategies should therefore be applied accordingly. This is the first study of the population
genetics of R. solani AG 3-PT in potatoes in South Africa and results may help to develop
knowledge-based disease management strategies in South Africa and elsewhere.