Mangrove ecosystems are widely recognised for their ecological and socio-economic importance, including coastal protection, carbon sequestration, and biodiversity safeguarding. However, beneath these visible ecosystem services lies an often-overlooked component of mangrove biodiversity: the microbial communities that inhabit the plants. Among these, endophytic fungi represent a hidden but potentially critical component of mangrove health, adaptation, and ecosystem functioning. Despite their ecological significance, the diversity and distribution of mangrove endophytic fungi remain poorly understood. Our study investigated the endophytic fungal communities associated with the leaves of two common mangrove species, Avicennia alba and Sonneratia alba, collected from multiple locations along the west coast of the Malay Peninsula. Using amplicon-based DNA metabarcoding, we characterised the fungal communities inhabiting leaf tissues and examined patterns of diversity across host species and geographic locations. Our analyses revealed a diverse assemblage of fungal taxa spanning multiple taxonomic groups, with community composition varying among sites and between host species. Several fungal lineages exhibited strong associations with particular mangrove populations, suggesting ecological specialisation and long-term host–environment interactions. Dominant taxa included members of the Ascomycota phylum, some of them commonly associated with coastal plants. Our findings demonstrate that each mangrove species and population harbours a distinct fungal community, representing a hidden layer of biodiversity that is not readily visible. These unique plant-microbe associations highlight that mangroves are more than the trees we see; they are complex biological systems shaped by long-standing ecological relationships. Consequently, the loss of natural mangrove stands may also result in the irreversible loss of specialised microbial communities, underscoring the importance of conserving existing mangrove ecosystems rather than assuming that restoration or relocation can fully replace them.

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