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Fungal endophytes play a pivotal role in tropical forest dynamics, influencing plant fitness through growth stimulation, disease suppression, stress tolerance, and nutrient mobilization. This study investigates the effects of region, leaf developmental stage, and tissue type on endophyte communities in tropical plants. Young and mature leaves were collected from 47 Rubiaceae species, and sapwood from 23 species, in old-growth forests of Golfito and Guanacaste, Costa Rica. Fungal diversity and composition were assessed through metabarcoding of the ITS2 nrDNA region. Most identified ASVs belonged to the phylum Ascomycota. The orders Botryosphaeriales and Glomerellales significantly contributed to endophytic assemblages, without detection of host-specific communities. We observed significant differences in species richness across regions, confirming distinct compositions through beta diversity. No statistically significant variances were found between mature and juvenile leaf tissues. In contrast, leaves exhibited richer and more diverse assemblages than sapwood. As plants experienced diverse environments over time and space, our results may be influenced by changing structural and chemical properties through ontogeny. Given the potential impact of these fungi on agricultural and forest ecosystems, ongoing research is crucial to discern the roles of hosts, endophytes, and other ecological mechanisms in apparent colonization patterns.