The fungus Aspergillus tubingensis is widely known from its use in industrial fermentation and other processes. More rarely, it is an opportunistic pathogen of humans or plants. In the present study, we found one rotten pomegranate fruit (Punica granatum) with black patches of rot and sporulation on the surface. Three A. tubingensis strains were isolated from this specimen. These were identified based on analyses of morphological characters and combined rDNA ITS, β-tubulin (tub2) and calmodulin (cal) loci. A pathogenicity test demonstrated that A. tubingensis is the pathogen of the rotten fruit of pomegranate. Therefore, the rotten fruits infected by A. tubingensis should be handled with care to avoid causing public hazard.