<p>The mangrove ecosystem exists on the margins of terrestrial and aquatic environments, contributing to its complexity and ecological dynamics. The interactions between microbial populations and mangroves enhance the productivity of the ecosystem. Research on mangrove microbial communities often relies on culture-dependent methods, which recover only a small fraction of fungi diversity. Fungal communities in mangrove were investigated by metabarcoding of the ITS1 region and the functional groups were inferred with FUNGuild. Two coastal locations in Tanzania were surveyed, focusing on mangrove leaves, roots, stems and soil. Ascomycota made up 87.6% of the detected ASVs, while basidiomycota occupied 8.6% and the remaining undetermined ASVs made up 3.8%. The Simpson’s index indicates high diversity across different compartments. FUNGuild analysis showed a higher presence of endophytic fungi, in the stem and root compartments, compared to other fungal types. This work provides insights into mangrove fungal communities, paving the path for further study.</p>