In October 2016, we collected samples of post-harvest anthracnose of papaya from Gangneung, Gangwon Province, Korea. Infected fruits first showed tiny light brown spots on their surface followed by development of sunken water-soaked lesions with black acervuli. Fungal pathogen was isolated from the infected fruits and cultured on potato dextrose agar (PDA) and synthetic nutrient agar (SNA) medium. For identification of the fungus, morphological assessment and sequencing analysis of 5.8S ribosomal DNA (ITS-5.8S rDNA) and three protein-coding genes: actin (ACT), chitin synthase I (CHS-1), and glyceraldehyde-3-phosphate dehydrogenase (G3PDH) were performed. Pathogenicity of the fungal isolate was confirmed according to Koch’s postulates. The results of morphological examination, pathogenicity tests, and the ITS-5.8S rDNA, ACT, CHS-1, and G3PDH sequences confirmed Colletotrichum truncatum as the causal agent. This study provides news information about C. truncatum isolated from post-harvest papaya in Korea.