Microorganisms in marine ecosystems are exposed to harsh conditions, thus such systems are of interest in bioprospecting for useful secondary metabolites. In Kenya, marine fungal organisms have not been explored for their therapeutic function. The characterization of these endophytic fungal species will provide further insight into the identification of the valuable bioactive compounds which will be the baseline in drug discovery. Endophytic microorganisms are fungi and bacteria that colonize inter- or intra-cellular spaces of plant tissues during at least one phase of their life cycle. The aim of the study was to isolate and identify the fungal endophytes that colonize mangroves. The fungal endophytes were isolated from the leaves, roots, and branches of different mangrove plants (Bruguiera gymnorrhiza, Heritiera littoralis, Xylocarpus granatum, Rhizophora mucronata, and Avicennia marina) from Mida creek, Tudor creek and Gazi bay using Point-Centered Quarter Sampling method and then, 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 spp. were the most prominent with a colonization frequency of 38.9 and 55.6% in root and branch tissues, respectively while 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%). 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.