Leaf-inhabiting endophytes belong to a diverse and active group of plant-associated fungi harboured in plant-rich tropical environments. Employing dilution-to-extinction cultivation and ITS sequencing, we assessed species richness, phylogeny and community composition of fungal endophytes within healthy leaves of three Ficus tree species (F. religiosa, F. benjamina, and F. elastica) naturally growing in the two Philippine forest reserves Mt. Makiling in Laguna and Mt. Palay–Palay in Cavite. Apart from a few basidiomycetes (3 orders, 6 genera), fungal isolates were abundantly ascomycetes (11 orders, 16 genera) and predominated by commonly known endophytic genera, such as Pseudocercospora, Phyllosticta, or Penicillium. Phylogenetic analysis revealed Capnodiales and Eurotiales as most OTU-rich clades and suggesting a high potential pathogen load in the investigated trees. Biodiversity analyses further revealed a higher similarity between the fungal species composition in the leaves of F. benjamina and F. elastica than to the one in F. religiosa. The observed higher abundance, species richness and similarity of the fungal community assemblage in the closely related host species F. benjamina and F. elastica, suggests an effect of host identity in structuring fungal endophytes community in the tropics.