The implementation of advanced irrigation systems, combined with modern agricultural techniques, allows for the establishment of almond plantations in new Mediterranean regions, namely the south of Portugal. The context of climatic changes, together with high-density, irrigated agricultural systems, may contribute to the appearance of almond tree diseases, and more specifically, fungal diseases. This study aims to understand the composition and distribution of fungal communities in different organs of symptomatic almond trees from a plantation in Beja, Alentejo. Samples of branches, trunks, and leaves have been collected from three symptomatic trees of two different cultivars (Vairo and Soleta). The samples have been surface-disinfected and inoculated in Petri dishes with Potato Dextrose Agar (PDA). The colonies are re-isolated into new Petri dishes with PDA and analyzed by molecular techniques, targeting nuclear rDNA's internal transcribed spacer (ITS) region for PCR amplification and Sanger sequencing. The results demonstrated differences in the fungal community between the different organs. Two fungal isolates were obtained from leaves and identified as Biscogniauxia mediterranea (sample from Vairo) and Preussia sp. (sample from Soleta). In the branch samples, B mediterranea, followed by Alternaria alternata, is the most representative fungus in both cultivars. Fusarium spp, Cystospora sp (includes pathogenic species associated with canker development in almond trees) and Trichoderma harzianum (an endophytic fungus known for its antagonistic capacity) are only present in trunk samples. In terms of the fungal community, we did not observe differences between the two cultivars, but we observed distinct patterns in community structure across organs. These results contribute to understanding the composition and distribution of fungal communities in almond trees, which allows for the design of new approaches for disease management and sustainable production.