Ficus carica Linn., a tender and juicy fruit, is susceptible to be damage and infected by microorganisms. Pathogenic fungi were isolated from infected site of Ficus carica Linn. during post-harvest storage and studied by morphological observation, rDNA internal transcribed spacer (ITS) sequence analysis of fungi and phylogenetic tree construction. The isolated pathogenic fungi were reinoculated back to the healthy fruits, and their symptoms were the same as those of the infected fruits. Four filamentous pathogenic fungi were isolated from infected fruit and leaf as Alternaria alternata (179^#), Fusarium odoratissimum (180^#), 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 Linn.. Biolog microbial identification system was used to analyse the carbon metabolic fingerprinting of four pathogenic fungi. The results showed that four strains had similar metabolic characteristics to 60 carbon sources, including 56 available carbon sources such as L-arabinose, D-cellobiose, α-cyclodextrin and ect., and 4 unavailable carbon sources such as N-acetyl-D-galactosamine, N-acetyl-β-D-mannosamine, L-trehalose and D-methyl lactate. This study provided a preliminary reference for biological features of pathogenic fungi and post-harvest control measures for Ficus carica Linn. diseases.