Botryosphaeria spp. are common endophytes and canker pathogens of many woody plants including eucalypts. Eucalyptus globulus, a species endemic to eastern Australia, dominates the plantation industry in Western Australia. Plantations are often adjacent to remnant native eucalypt forest and each vegetation type (plantation or forest) could harbour pathogens to which the other has not been exposed. A survey of Botryosphaeria spp. associated with E. globulus and native Eucalyptus spp. in Western Australia revealed four distinct culture morphologies to be present among 147 isolates. Representative isolates of each type were characterised based upon morphological features and comparisons of a combined DNA dataset including the internal transcribed spacer, a part of the β-tubulin gene and part of the elongation factor 1α (EF-1α) gene. The majority of the isolates (95%) were Botryosphaeria australis. Of the remaining isolates, one was Botryosphaeria parva, three were Dichomera eucalypti (an anamorph of an unknown Botryosphaeria sp.) and the remaining four isolates were identified as representative of a new species described here as Fusicoccum macroclavatum sp. nov. The new species resided alone in a well supported clade and differed morphologically from other Fusicoccum spp. by having large, predominantly elongate–clavate conidia. Fusicoccum macroclavatum sp. nov. was the most pathogenic of the four species, and its rare occurrence only on eucalypt species endemic to eastern Australia suggests that this species has been introduced to Western Australia.