After recent changes to the taxonomy of the Botryosphaeriaceae species with diplodia-like (= dark, ovoid, often pigmented) conidia are considered to belong to at least three genera including Diplodia, Lasiodiplodia and Dothiorella. In a recent molecular phylogenetic study it became apparent that two groups of isolates with diplodia-like conidia required taxonomic revision. One group of isolates originated from Cupressus sempervirens in Greece and Cyprus and had been identified as D. pinea f. sp. cupressi based on morphological characteristics. The other isolates originated from a Casuarina sp. in Australia and were superficially similar to those in the first group based on their morphologically similar diplodia-like conidia. The aim of this study was to resolve the taxonomy of these two groups of isolates by combining the information from the multiple gene genealogies with morphological characters. The results showed that the isolates from C. sempervirens in Greece and Cyprus represent D. cupressi. The isolates from Casuarina in Australia belong to the more distantly related genus Dothiorella and represent a distinct species that is described here as Do. casuarini sp. nov.