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Syzygium samarangense (Wax apple) is an important tropical fruit tree with high economic and nutrient value and is widely planted in the tropics or subtropics of Asia. A water-soaked brown lesion was observed in the mature fruits of ornamental wax apples in Chiang Rai Province, Thailand. A fungus with morphological characters similar to Lasiodiplodia was consistently isolated from symptomatic fruits. Phylogenetic analyses based on ITS, LSU, tef1 and tub2 revealed that our isolates were closely related to but phylogenetically distinct from Lasiodiplodia rubropurpurea.Morphological comparisons indicated that pycnidia and conidiogenous cells of our strains were significantly larger than L. rubropurpurea. Comparisons of base pair differences in the four loci confirmed that the species from wax apple was distinct from L. rubropurpurea and a new species, L. syzygii sp. nov., is introduced to accommodate it. Pathogenicity tests confirmed the newly introduced species as the pathogen of this water-soaked brown lesion disease in wax apples.