Endophytic fungi enhance plant growth and improve tolerance to abiotic and biotic stress. Calicotome spinosa is an important medicinal plant that occupies the area of Tizi-Ouzou and is considered a nonflammable plant that maintains this ecosystem and regenerates degraded substrates. However, the knowledge about the endogenous fungal assembly of C. spinosa remains underexplored. Therefore, this study aimed to isolate and determine the fungal communities inhabiting the C. spinosa leaves endosphere using morphological and molecular identification methods. Morphological identification revealed the presence of Alternaria, Cladosporium, Mucor, Neoscytalidium, Rhizoctonia, Rhodotorula, Phoma, Penicillium, and Trichophyton genera. Molecular analysis of the selected phylogenetic markers' nucleotide sequences detailed the previous one and discovered the following: Biscogniauxia mediterranea, Schizophyllum commune, Penicillium polonicum, Athelia bombacina, Chaetomium globosum, Penicillium brevicompactum, Coriolopsis sp., Coprinellus sp., Aspergillus chevalieri, Aspergillus wentii, Canariomyces microspores, Alternaria alternata, Canariomyces notabilis, Rosellinia sp., Penicillium sp., and Alternaria sp. The taxonomic knowledge gained here for the first time about the group of endophytic fungi associated with the ethnomedicinal plant growing in Algeria, and the disposition of these fungi isolates provides a basis for further research into understanding the functions they may have in the plant. These isolates are therefore a source of potential candidates for further research into their possible applications as beneficial microorganisms in ecology, environmental and plant protection, and sustainable agriculture.