A new fungal species, Pestalotiopsis samarangensis, was isolated from fruit rot in Syzygium samarangense from markets in Chiang Mai and Chiang Rai provinces, Thailand. Initially small, circular, black, slightly sunken spots developed on fruits. Later, the spots enlarged rapidly, became sunken, and resulted in a soft decay of the fruit flesh. Molecular analysis of the ITS, β-tubulin, and tef1 combined gene sequences distinguish P. samarangensis from other species in the genus. Pathogenicity testing proved that wounding triggers the disease symptoms and thus careful handling of fruits during transport and storage helps to prevent the disease.