Our study highlights the importance of endophytic fungi in mangrove ecosystems and emphasizes the potential of metagenomics to uncover their diversity and ecological functions. A systematic literature review using available and widely used databases: Google Scholar, Web of Science, PubMed, NCBI, ASM, and BioMed revealed a significant gap in research regarding these symbiotic microorganisms despite their importance in mangrove ecosystems.

The identified publications span the period of 2012 to 2024 and represent the known body of knowledge on the use of metagenomics methods in the study of endophytic fungi in mangroves. These studies were conducted in different areas of the world: New Caledonia (France), Mumbai (India), Taiwan, and Guangdong Province (China), and focus on the key mangrove species: Acanthus ilicifolius, Avicennia marina, Rhizophora stylosa, Aegiceras corniculatum, Bruguiera gymnorrhiza, Kandelia candel, and Excoecaria agallocha. Results of this study illustrate the diverse ecological contexts in which endophytic fungi exist, but also suggest that additional research is needed to fully understand the extent of fungal diversity among other mangrove species and regions.

 By synthesizing provided studies in the current research and identifying knowledge gaps, this review establishes directions for future development of deeper understanding of the complex world of mangrove endophytic fungi.