Occupational exposure to grain dust is associated with both acute and chronic effects on the airways. However, the aetiology of these effects is not completely understood, mainly due to the complexity and variety of potentially causative agents to which workers are exposed during cereals process. In this study, we characterized the mycobiome during different steps of wheat processing-harvesting, grain unloading and straw handling-and compared it to mycobiomes of domestic environments-rural and urban. To do so, settled dust was collected at a six month interval for six weeks in the close proximity of 142 participants, 74 occupationally exposed to wheat dust-freshly harvested or stored-and 68 not occupationally exposed to it. Fungal community composition was determined in those samples by high-throughput sequencing of the primary fungal barcode marker internal transcribed spacer 1 (ITS1). The comparison of different mycobiomes revealed that fungal richness, as well as their composition, was much higher in the domestic environment than at the workplace. Furthermore, we found that the fungal community composition strongly differed between workplaces where workers handled freshly harvested wheat and those where they handled stored wheat. Indicator species for each exposed population were identified. Our results emphasize the complexity of exposure of grain workers and farmers and open new perspectives in the identification of the etiological factors responsible for the respiratory pathologies induced by wheat dust exposure.