Potato skin blemishes with known causes (typical blemishes) are manageable in contrast to those with unknown causes (atypical blemishes). This study investigated possible fungal causal agents of atypical tuber blemishes in South Africa and Zimbabwe through isolation and pathogenicity testing. Several fungal genera were isolated from elephant hide, corky cracks, star-shaped lesions, circular corky lesions, raised corky spots, enlarged lenticels and russetting. Koch’s postulates could not be fulfilled with most of the isolates except for binucleate Rhizoctonia (BNR) AG A, Macrophomina phaseolina and Rhizoctonia solani AG 3-PT. BNR AG A isolates from South African tubers of cv. Up-to-Date reproduced circular and linear defects on tubers. M. phaseolina isolates inoculated on South African cv. Mondial reproduced dark, circular lesions around lenticels conforming to typical symptoms of charcoal rot on potato tubers. R. solani AG 3-PT isolates reproduced corky cracks with elephant hide and black scurf with similar aggressiveness on cvs Mondial (South Africa) and Diamond (Zimbabwe). This is the first report of charcoal rot caused by M. phaseolina and of tuber defects caused by BNR AG A on potato in South Africa. This is also the first report of tuber cracking and elephant hide caused by R. solani AG 3-PT on potato in Zimbabwe. The findings from this work are crucial in formulating control strategies against these pathogens in order to improve potato tuber quality on the market.