The genus Ceratocystis includes many important tree pathogens and agents of sap stain. These fungi have a global distribution and commonly infect wounds on trees. During a survey of wound-infecting pathogens in the genus Ceratocystis on plantation-grown Acacia mangium trees in Indonesia, several isolates resembling Ceratocystis moniliformis sensu lato (s.l.) were obtained. The aim of this study was to identify these isolates and to test their pathogenicity on commercially grown Acacia spp. in the country. Use was made of morphology and comparisons of DNA sequence data for the ITS, β-tubulin, and transcription elongation factor 1-α gene regions to identify the isolates. Three previously undescribed species in the C. moniliformis s.l. species complex were identified and are described here as C. inquinans sp. nov., C. sumatrana sp. nov., and C. microbasis sp. nov. Pathogenicity trials on Acacia mangium and A. crassicarpa in the greenhouse and in the field indicated that all three species have the potential to infect A. mangium and A. crassicarpa, although they are not considered important pathogens.