Three fungal species responsible for anthracnose canker, perennial canker, and bull's-eye rot of apple have been considered members of the genus Pezicula for a number of years. Recent studies, however, have provided evidence to (re-)classify these species as Neofabraea. There has been a long historical debate regarding the taxonomy of two of these fungi. In Europe, both Neofabraea malicorticis and N. perennans have generally been considered N. malicorticis, while in North America a species distinction has been maintained. Phylogenetic analyses of Neofabraea isolates were based on DNA sequences of the internal transcribed spacer region of nuclear rDNA (38 isolates), the mitochondrial rDNA small subunit (partial; 48 isolates), the β-tubulin gene (partial; 25 isolates), and a combined data set (21 isolates). Our work provides evidence for the existence of four distinct Neofabraea apple pathogens including N. malicorticis, N. perennans, N. alba, and a putative new Neofabraea species that was isolated in both Europe and eastern North America. Our results indicate that the primary Neofabraea species causing tree cankers and bull's-eye rot in North America are N. malicorticis and N. perennans in the west, and N. alba in eastern Canada. N. perennans, N. alba, and the undescribed Neofabraea species were found in Europe but the presence of N. malicorticis was not confirmed by our limited sampling. Inclusion of Rosa spp. in the host range of N. malicorticis is merited.