Mangroves are distinct ecosystems that harbor a rich biodiversity. Fungal endophytes play an important role in the biogeochemical processes within these ecosystems, making them an essential ecological element. Eleven grey mangrove stands on Egypt's Red Sea coast were examined to assess the diversity of culturable endophytic fungal populations. 450 endophytic fungal isolates were obtained from pneumatophores (60.9%) and leaves (39.1%) of Avicennia marina. Significant differences were observed in both colonization and isolation rates (P < 0.001). In every research site, the rates of colonization in pneumatophores were greater than in leaves. Shannon-Wiener diversity indices varied significantly among the studied sites, ranging from 1.50 to 2.19 (P < 0.001). The highest level of diversity was observed in Marsa Alam, Qalaan, and Safaga, while the lowest was reported for the Sharm Bahry mangrove. Out of the 450 isolates, 354 (79%) were identified to at least the genus level, whereas the rest were unidentified morphotypes, comprising 31 black yeasts and 65 mycelia sterilia. The identified isolates were classified into two phyla: Ascomycota was the most abundant, accounting for 98.3% of the isolates, while Basidiomycota accounted for only 1.7%. Fourteen genera belonging to four taxonomic classes, namely Sordariomycetes, Eurotiomycetes, Dothideomycetes, and Agaricomycetes, were recognized, with Chaetomium, Aspergillus, and Penicillium being the predominant. Based on available literature, this is the first comprehensive report documenting the biodiversity of mycoendophytes associated with A. marina in Egypt. It provides in-depth information on their occurrence and distribution within mangrove ecosystems at eleven locations along the Egyptian Red Sea coastline.