Blueberry has been a burgeoning fruit in China in recent years, but its perishable nature places a constant strain on industrial development. To determine the pathogens infecting blueberry fruits, diseased samples were collected from Guizhou and Fujian Provinces. Isolates from the samples were identified by morphological characterization and phylogenetic analyses. Pathogenicity assays were conducted on fresh blueberry fruits using spore suspensions. Sixteen isolates were identified as seven species, namely, Botryosphaeria dothidea, Botrytis cinerea, Cladosporium guizhouense, Colletotrichum fioriniae, Diaporthe anacardii, Fusarium annulatum, and Neopestalotiopsis surinamensis, and their pathogenicity on blueberry fruits were confirmed following Koch’s postulates. The current study reported Cladosporium guizhouense, Fusarium annulatum, and Neopestalotiopsis surinamensis for the first time on blueberry. The study (1) demonstrated that fruit rot disease results from a mixed infection of multiple pathogens; and (2) expanded the understanding of causal agents of blueberry fruit rot during the growth stage, highlighting their potential as latent pathogens that contribute to post-harvest losses. Relevant results provide a reference for the etiological research and disease management in blueberry fruit diseases.