The study of filamentous fungi is fundamental not only to extend their biotechnological applications, but also to develop new drugs to fight pathological species. Morphological analyses are particularly relevant when investigating their development and differentiation. The need to maintain the orientation of hypahe and the presence of a cell wall, which hampers the sample infiltration with cryoprotectants and other reagents necessary to preserve the cell ultrastructure, creates difficulties with the use of electron microscopy (EM). Here, we present an immunoelectron microscopy (IEM) procedure that combines the Tokuyasu protocol adapted to yeast and the flat-embedding technique. While the first method leads to a fine resolution of the ultrastructure of Aspergillus nidulans because of both the cell wall permeabilization and the negative membrane coloration, the second permits us to preserve the spatial distribution of the hypahe of this fungus. The presented data demonstrate the advantages of this combination and the unprecedented potential of this relatively simple and rapid protocol in resolving the morphology of filamentous fungi and performing localization studies.