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The interaction of mangrove trees with endophytic microorganisms contributes to the successful establishment of these plants in the challenging intertidal environment. The red mangrove, Rhizophora mangle L. (Rhizophoraceae), is one of the dominant species in mangrove ecosystems and is characterized by the provision of several ecologically relevant services. In this work, we integrated metagenomics and metatranscriptomics to perform a robust characterization of the community of endophytic microorganisms associated with R. mangle leaf and root tissues. The microbiota were characterized at taxonomic and functional levels, and abundance and gene expression profiles were compared between these two plant tissues. We found that the endophyte community consisted mainly of bacteria and eukaryotes, which were the most active groups at the transcriptional level, while archaea and viral groups were identified in lower abundance and expression. In addition, the results show that the community of endophytic microorganisms changes depending on the tissue type, with root-associated microorganisms being the most abundant at the metagenome level and active at the metatranscriptome level. It was also found that R. mangle endophytes actively contribute to key functions for adaptation to an intertidal ecosystem with high human intervention, such as salinity tolerance and degradation of heavy metals and xenobiotic compounds. Thus, according to the functions found and contributed by the endophyte community of red mangrove leaf and root tissues, it can be concluded that these microbial communities are crucial for the survival of R. mangle in the extreme environment of mangrove forests. This study provides a solid basis for future research aimed at understanding the role of plant-endophyte interactions.