Anthracnose and crown rot are the main diseases affecting bananas after harvest. These diseases are mainly caused by Colletotrichum musae (anthracnose) and to some extent by various Fusarium species forming a fungal complex (crown rot). A water-borne spore trap was used to collect and quantify all inocula reaching banana bunches from flowering to harvest. The pattern of natural contamination was characterized by a peak from 25 to 40 days after bunch emergence, with a strong decline until harvest. Both Colletotrichum and Fusarium species had the same dynamics during bunch growth. Flower parts are the main inoculum source for Fusarium; both flower parts and the last bunch bract are important sources for Colletotrichum. Primary inoculum could reach flower parts and the last bunch bract through rain splash of conidia, transport by insects or aerial dissemination of ascospores. Sporulation occurring on the young flower parts and on the last bunch bract provides heavy secondary inoculum. The consequences for control strategies are discussed.