Bark canker, wood discoloration, and wilting of the duku tree (Lansium domesticum) along the watershed of Komering River, South Sumatra Province, Indonesia first appeared in 2013. The incidence of tree mortality was 100% within 3 years in badly infected orchards. A Ceratocystis species was consistently isolated from the diseased tissue and identified by morphological and sequence analyses of the internal transcribed spacer (ITS) and β-tubulin regions. Pathogenicity tests were conducted and Koch’s postulates were confirmed. The fungus was also pathogenic on Acacia mangium, but was less pathogenic on mango. Partial flooding was unfavourable for disease development. Two described isolates (WRC and WBC) had minor variation in mor- phology and DNA sequences, but the former exhibited a more pathogenic on both duku and acacia. The ITS phylogenies grouped the most pathogenic isolate (WRC) causing wilting of the duku tree within the aggressive and widely distributed ITS5 haplotype of C. fimbriata.