Ficus carica Linn, a tender and juicy fruit, is susceptible to damage and infection caused by microorganisms. In this work, pathogenic fungi were isolated from infected Ficus carica fruit and leaves during post-harvest storage. Based on morphological, internal transcribed spacer (ITS) sequence analysis of fungal isolates enabled species delimitation and their position on the phylogenetic combined tree, four pathogenic fungi were isolated from infected fruit and leaf. All isolates may have caused similar symptoms of the disease in healthy Ficus carica fruit. Four strains were identified as Alternaria alternata (179#), Fusarium odoratissimum (180#), as Colletotrichum endophyticum (181#), and Mucor racemosus (182#), among which Fusarium odoratissimum , Colletotrichum endophyticum and Mucor racemosus were the first report of causing disease of Ficus carica fruit. According to biolog microbial identification system, the carbon metabolic fingerprinting showed that four strains had similar metabolic characteristics to 60 carbon sources, including 56 available carbon sources such as L-arabinose, D-fibrinose and α -cyclodextrin, and 4 unavailable carbon sources such as N-acetyl-D-galactosamine, N-acetyl-β -D-mannosamine, L-trehalose and D-methyl lactate. This study provides a preliminary reference for biological features and post-harvest control measures for Ficus carica fruit diseases.