The ascomycete genus Ceratocystis has a broad geographic distribution and includes pathogens of a wide range of mostly woody hosts. Black rot of Colocasia esculenta (taro), a popular cultivated root crop in China, is caused by a species of Ceratocystis broadly treated as C. fimbriata sensu lato. Recently, isolates of Ceratocystis were obtained from black rot lesions on C. esculenta corms in two Chinese provinces. Sequence comparison of the ITS, partial β-tubulin, TEF-1α, MS204 and RPBII gene regions were used to identify these isolates and compare them to other Ceratocystis species. Furthermore, the diversity of Ceratocystis species in the Asian-Australian clade (AAC) was investigated using 23 microsatellite markers. Results showed that the isolates from C. esculenta represent a novel species, which is morphologically and phylogenetically different to closely related species in the AAC, and is described here as Ceratocystis changhui sp. nov. In microsatellite analyses, this new species also emerged as distinct from others in the AAC. Inoculation tests showed that C. changhui sp. nov. is a virulent pathogen of C. esculenta corms, but produces only small lesions on Eucalyptus grandis and Eriobotrya japonica.