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Imported kiwifruit affected by soft rot on Shanghai fruit market was selected for pathogen isolation and identification. The pathogenicity of different strains was compared. Morphological detection was combined with molecular tools to identify the main pathogenic strains as well as their biological characteristics. The results showed that Phomopsis was the main pathogen causing soft rot, and Phomopsis vaccinii (P. vaccinii) had the highest pathogenicity. Soft rot in kiwifruit caused by P. vaccinii was effectively inhibited under 5 C. This article is a first report of the pathogens causing soft rot in kiwifruit in Chinese market. Valuable experimental evidence is provided for the study on the pathogens carried by kiwifruit imported from New Zealand and on the occurrence of soft rot on the market.