Postharvest apple rot causes severe economic losses and lowers apple quality, and is one of the most important limiting factors of apple exports. Apples with rot symptoms were sampled from Geochang, South Korea. Isolation of the causal fungus was performed by culturing small pieces of diseased tissues on potato dextrose agar. Two different rot genera, Fusarium and Alternaria, were identified according to their morphological characteristics. To confirm the identity of the causal fungus, we sequenced the DNA of the complete internal transcribed spacer(ITS) rDNA gene region and translation elongation factor 1-alpha(EF1-α) region. Koch’s postulates were supported by pathogenicity tests conducted on apple fruit. Based on mycological characteristics, molecular identification, and pathogenicity tests, the two fungi were identified as Fusarium tricinctum and Alternaria alternata. To the best of our knowledge, this is the first report of postharvest apple rot caused by F. tricinctum and A. alternata in South Korea.