| Summary: | Rot disease is a serious disease in pomegranate (<i>Punica</i> <i>granatum</i> L.) plantations in China. This disease usually weakens tree vigor, and seriously reduces the ornamental value, fruit yield, and quality. A better understanding of the pathogen that causes a disease is important for its control. Thus, the aims of this study were to isolate and identify the pathogen causing rot disease and to explore substances for its biological control. In this study, the morphology of the hyphae and spores of the pathogens was observed, and the pathogens were identified by morphological characteristics and the internal transcribed spacer (ITS) regions of their rDNA. Furthermore, the activity of an aqueous garlic extract as antifungal treatment for the identified pathogens was assessed. The results showed that the pathogens causing soft rot and dry rot in ‘Xinjiang Big Seed’ pomegranate were most probably <i>Aspergillus niger</i> and <i>Botryosphaeria dothidea</i>, respectively. In addition, the pathogenicity of <i>A. niger</i> was stronger than that of <i>B. dothidea.</i> The aqueous garlic extract had a strong antifungal effect on both pathogens by inhibiting mycelium growth in vitro, and the minimum inhibitory concentrations against <i>A. niger</i> and <i>B. dothidea</i> were 7.5 mg/mL and 10 mg/mL, respectively.
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