Anthracnose is one of the leading causes of quality losses in banana fruit. It is caused by several species in the genus Colletotrichum. In the Philippines, Colletotrichum musae has long been known as the only anthracnose pathogen of banana in the Philippines, but molecular characterization is yet to be done. Further, little is known of cultivar susceptibility to anthracnose in popular banana cultivars. Here we provide evidence for C. musae as a postharvest anthracnose pathogen of banana cv. Cavendish, presents the first molecular characteristics of C. musae PHBN0002, and demonstrates the susceptibility of three popular banana cultivars to postharvest anthracnose. The pathogen was isolated from anthracnose-infected fruit of cv. Cavendish with morphological characteristics resembling to C. musae. The ITS-rDNA, GAPDH and ACT sequences of the fungus had high similarities to that of the authentic sequences of epitype specimen of C. musae. In controlled unwounded detached-fruit assays, fruit of cv. Lakatan, Latundan and Saba developed anthracnose seven days post inoculation of C. musae. The results strengthen the knowledge of C. musae as the anthracnose pathogen of banana in the Philippines and demonstrates the ability of the fungus to cross-infect to popular banana cultivars. This study may lead to further characterization of the genetic variability of C. musae from different banana growing regions in the country, which is one of the key elements in developing effective and durable control measures.