Aims To identify cultivable filamentous fungi before ensiling, after silage conservation, in farm‐silos covered with two different plastic films (polyethylene (PE) vs biodegradable (MB)), as well as after aerobic exposure of whole‐crop corn silage. Methods and Results Molecular techniques coupled with traditional microbial counting were utilized to identify the predominant fungal species. The cultivable fungal population changed remarkably from harvesting to silo opening. Anaerobiosis and low pH reduced mould count and the presence of Fusarium species both under PE and MB film. However, in the peripheral areas of the silo, where air penetration could not be completely prevented, the fungal population did not decrease. The predominant fungal species after aerobic exposure of silage was Aspergillus fumigatus, without differences between the two plastic films. Conclusions Maintenance of anaerobiosis and a low pH also in the upper layer of the silo reduce the risk of mould growth during corn silage feed‐out. Significance and Impact of the Study Even if the new MB plastic film did not completely maintain the anaerobiosis in the upper layer of silage, the overall silage quality was not compromised and was similar to that observed under PE, indicating that the development and use of MB film to cover silage is promising, but needs some improvement.