Aims <p>Leaf-associated microorganisms are intimately related to plant diseases. The majority of faba bean leaf diseases are induced by fungal communities. Nevertheless, limited studies have been presented on the structure and assembly of the fungal communities in faba bean plants.</p> Methods <p>This study investigated the structure and assembly of the fungal communities in the phyllosphere and endosphere of healthy and diseased five germplasm resource faba bean plants with ITS amplicons using the Illumina high-throughput sequencing platform.</p> Results <p>The fungal community in both phyllosphere and endosphere samples, as well as healthy and diseased, displayed significant distinctions. Additionally, substantial variations were identified in the fungal communities of different germplasm resources and the degrees of illness of phyllosphere and endosphere samples. Distinct differences were also found in the species richness of phyllosphere and endosphere samples among different illness degrees. The Mortierellomycota was the predominant phylum in the healthy samples. The dominated genus of diseased samples were <i>Vishniacozyma</i> and <i>Cystofilobasidium.</i> The <i>Apiotrichum</i> was significantly enriched in healthy endosphere samples. The network structure of the healthy phyllosphere samples was more sophisticated and stable, with the genus <i>Ganoderma</i> being the core fungal taxa within the healthy phyllosphere samples. The deterministic processes dominated the assembly of healthy samples fungal communities, whereas stochastic processes mainly influenced the assembly of fungal communities in the diseased phyllosphere samples.</p> Conclusions <p>Overall, this research contributes to understand the correlation between leaf microbiota and hosts, and provides theoretical support for the healthy plant growth and disease prevention of faba beans.</p>