Fruit pathogens are currently one of the main factors involved in quarantine-related market access. Unconfirmed South African records pertaining to the presence of the causative agent of European canker of apples, Neonectria ditissima, have been the cause of many disputes regarding its status as a quarantine pest in this country. To clarify this issue, the identity of fungal isolates that were presumed to be N. ditissima, were verified by making use of species-specific PCR primers designed for N. ditissima. The isolates were obtained from symptomatic apple trees in the major apple-producing areas in South Africa. These data were supplemented by a morphological reexamination of all six previous herbarium specimens presumed to be N. ditissima. The results revealed that none of the samples tested positive for N. ditissima, nor were any of the six herbarium specimens representative of Neonectria species. This study represents the first attempt to resolve the status of N. ditissima in South Africa by means of a molecular approach, and our findings support the current regulated status of N. ditissima in South Africa.