Mangrove-associated fungal endophytes (MFE) produce structurally diverse secondary metabolites with promising pharmaceutical applications. In our effort to search for these valuable fungi, reported herein is our isolation and molecular identification of fungal endophytes associated with mature leaves of the host mangrove Rhizophora mucronata. The isolated MFE were characterized based on their colonial growth on three culture media -potato dextrose agar (PDA), Czapek Dox agar (CDA), and malt extract agar (MEA), and these were grouped into 16 morphospecies. Analysis of the ITS genes confirmed the identities of the isolated mangrove fungal endophytes as belonging to the genera Aspergillus, Cladosporium, Curvularia, Diaporthe, Fusarium, Nigrospora, Penicillium, Pestalotiopsis, and Schizophyllum. Our study showed the species richness of fungal endophytes associated with Philippine mangroves.