Mangrove forests are among the most biologically diverse ecosystems in the planet and hosts to a number of mangrove-associated fungi. The Philippines with more than 40 mangrove species is undeniably rich with numerous plants that could be host to lower fungi such as oomycetes and thraustochytrids and to higher fungi such as ascomycetes and basidiomycetes. Early studies on mangrove-associated fungi in Philippines center on driftwoods along the mangrove intertidal zones. However, recent studies also explored the fungal endophytes and thraustochytrids associated with the healthy and senescent mangrove leaves. These mangrove-associated fungi are tapped for various biotechnological applications such as production of enzymes and as sources of high amounts of fatty acids. Fungi from mangroves are also promising sources of bioactive secondary metabolites with antibacterial and cytotoxic activities.