Diplodia species are known as pathogens on many woody hosts, including fruit trees, worldwide. In this study a collection of Diplodia isolates obtained mostly from apple and other Rosaceae hosts were identiﬁed based on morphological characters and DNA sequence data from ITS and EF1-α loci. The results show that the diversity of species associated with twig and branch cankers and fruit rot of apples is larger than previously recognised. Four species were identiﬁed, namely D. seriata and D. malorum (which is here reinstated for isolates with D. mutila-like conidia). Diplodia intermedia sp. nov. is closely related to D. seriata, and D. bulgarica sp. nov. is morphologically and phylogenetically distinct from all Diplodia species reported from apples.