Microorganisms in marine ecosystems are exposed to harsh conditions, thus such systems are of interest in bioprospecting for useful secondary metabolites. In this study, endophytic fungi were isolated from the leaves, roots, and branches of mangrove species (Bruguiera gymnorrhiza, Heritiera littoralis, Xylocarpus granatum, Rhizophora mucronata, and Avicennia marina) from Mida creek, Tudor creek and Gazi bay using standard protocol and morphologically characterized. A total of 76 fungal isolates were obtained and identified using macro and micro morphological features. The isolates were affiliated with eight different genera (Aspergillus, Cladosporium, Nigrospora, Fusarium, Alternaria, Lasiodiplodia, Chaetomium, and Penicillum). Aspergillus species were the most prominent with a colonization frequency of 38.89% and 55.56% in root and branch tissues, respectively. Chaetomium species were the least frequent appearing only in one branch tissue. Mida creek had the highest total number of endophytic isolates [52.6%] followed by Gazi bay [27.6%]. The majority [30.3%] of the endophytic fungal isolates were obtained from Avicennia marina. The results indicate that mangrove species are a source of diverse endophytic fungi that may have useful biotechnological applications.