Mango (Mangifera indica) sudden decline is an important disease in Oman, which is closely associated with infections by Ceratocystis fimbriata and Lasiodiplodia theobromae. Another Ceratocystis species has also been found associated with symptoms on diseased trees. In this study, we identify that Ceratocystis based on morphology and DNA sequences. Morphological comparisons showed that the fungus from dying mango trees in Oman is similar to C. moniliformis. Both fungi have distinct hat-shaped ascospores, disc-shaped plates at the bases of the ascomatal necks and spines on the ascomatal bases. However, comparison of DNA sequences for ITS1-2, the 5.8S RNA gene, the beta-tubulin gene, and Transcription Elongation Factor (EF1-alpha) gene, confirmed that the fungus from Oman is distinct from C. moniliformis and other related species. Phylogenetically, this fungus formed one of four strongly supported sub-clades. The other sub-clades included isolates of C. bhutanensis, C. moniliformis and C. moniliformopsis, respectively. Based on morphological characteristics and differences in DNA sequences for three gene regions, we conclude that the Ceratocystis sp. from wounds on mango in Oman is a new species, for which we provide the name Ceratocystis omanensis sp. nov.