Black mould, caused by Aspergillus niger, is the main fungal disease affecting date fruits. Symptoms develop inside the fruit, at the inner space between the pulp and the seed. This study focuses on the aetiology of black mould disease in Medjoul fruit. We followed symptom appearance naturally and after artificial A. niger inoculation at different development and maturity stages. Symptoms developed in only a short period during early fruit ripening. However, fruits were commonly colonized at earlier stages of development. Artificial inoculation of flowers and setting fruitlets increased the level of fruit colonization, while fungicide spraying at these stages decreased colonization. Several weeks following flower inoculation by A. niger, mycelium could be detected on degenerating stigmas and carpels as well as between the fruit and the calyx. Following inoculation with an A. niger strain expressing green fluorescent protein (A. nigerGFP), the pathogen was detected on stigmas of setting fruitlets but not within the stigmatic tissue or the transmitting tract of the carpel. The A. nigerGFP strain was detected during fruit development below the base of the large fruitlets and above the calyx surrounding the vascular bundle leading into the fruit. The results suggest that A. niger can infect and colonize flowers and setting fruitlets, grows on the degenerating carpels, and remains latent at a protected site at the base of the fruit until ripening. It then induces the typical black mould symptoms. The significance of these results for developing means to cope with the disease is discussed.