This study aimed at the isolation and characterizion of endophytic fungi inhabiting halophytes (Nypa fruticans and Rhizophora racemosa) growing in mangrove ecosystem of Akwa Ibom State, Nigeria. The physico-chemical parameters of the rhizospheric soils revealed EC (5.11, 5.41 and 5.01 dS/m), pH (5.1, 5.0 and 5.2), Na (2.26, 2.28 and 2.15 Cmol/kg) respectively. The identified strains were categorized into the phyla Ascomycota. At the genus level, Aspergillus (16 strains) accounted for the highest proportion followed by Penicillium (13 strains) and Fusarium (8 strains). The genera of the endophytic fungi isolated from the halophytic plants were Talaromyces, Aspergillus, Neosartorya, Purpureocillium, Fusarium and Penicillium. The six species isolated and characterized were; Talaromyces albobiverticillius (1), Aspergillus aculeatus (2), Aspergillus fumigatus (3), Fusarium equiseti (4) and Penicillium citrinum (5 and 6). The result from this study demonstrates the existence of fungal endophytes which have great potential in plant productivity. Additionally, this work creates a baseline study in the said study area; this will enable further researches emphasizing the importance of endophytic fungi in agricultural sectors as an eco-friendly biofertilizer to improve plant growth performance and defense as an alternative to inorganic fertilizers which have detrimental effects on both plants and the environment.