Abstract:According to Koch‘postulates, the pathogenic fungus causing a destructive decay of stored pomegranate fruitswas isolated and confirmed. After cloning the internal transcribed spacer ( ITS) region of the isolate using polymerase chain reaction ( PCR) technique, the gene sequence of ITS region of isolate were determined. Using Blast System, the difference of the gene sequences between the isolate and the fungus in EuropeanMolecular B iology Laboratory Genbank was compared. The result showed that the isolate fungus and B otryosphaeria dothidea share more 99% homology sequence. Therefore, the isolated funguswas identified as B otryosphaeria dothidea. The symp toms of B otryosphaeria dothidea causing fruit rot are same with other fungus in other reports. This paper is the first report about B otryosphaeria dothidea causing pomegranate rot. In addi tion, the disease cycle and the ep idemiology of B otryosphaeria dothidea were investigated in order to control the decay of stored pomegranate fruits.