Fusarium boothii forms part of the Fusarium graminearum species complex (FGSC), the important grain pathogen group that causes Gibberella ear rot of maize and Fusarium head blight of wheat. It is known to infect many grain crops such as maize, wheat and barley. Moreover, this pathogen is a 15-ADON mycotoxin producer and thus of concern for stored grains and grain products. During endophyte isolations in the Hoopstad area of the two unrelated trees, pecan and camel thorn, isolates of the FGSC constituted a dominant part of the Fusarium isolates obtained. Pecan (Carya illinoinensis) is a rapidly developing industry in the semi-arid to arid regions of South Africa, while camel thorn (Vachellia erioloba) is a dominant native tree in the same areas. DNA sequence comparisons of the translation elongation factor 1-α and β-tubulin gene regions clearly showed that these isolates were F. boothii. This study thus represents the first report of this grain pathogen from unlikely tree hosts, and only the second report of a species in the FGSC from trees, the other being that of Fusarium acacia-mearnsii. The unexpected occurrence of F. boothii in hosts other than grain could represent an important gap in our understanding of the epidemiology, geographical occurrence and movement, and genetic pool of this important pathogen. It also raises the question of whether other species in the FGSC could have unexpected host associations.