Microbial communities are an important component of mangrove ecosystems. In order to reveal the diversity of endophytic fungi in the mangrove ferns and in China, the internal transcribed spacer (ITS) regions of endophytic fungi in four plant tissues (leaves, petioles, roots, and rhizomes) from three locations (Zhanjiang, Haikou, and Wenchang) were sequenced. The richness, species composition, and community similarity were analyzed. The main results are as follows: the dominant fungi in and belonged to the phyla Ascomycota and Basidiomycota, accounting for more than 75% of the total identified fungi; in terms of species composition at the operational taxonomic unit (OTU) level, the endophytic fungi in were more diverse than those in , and the endophytic fungi in rhizomes were more diverse than in other tissues. In Zhanjiang, both and showed the richest diversity of endophytic fungi, both at the OTU classification level and in terms of species composition. Conversely, the richness of endophytic fungi in the samples of from Wenchang and Haikou is extremely low. The regional differences in dominant fungi increase with the degrading of taxonomic levels, and there were also significant differences in the number of unique fungi among different origins, with Zhanjiang samples having a larger number of unique fungi than the other locations. There were significant differences in the dominant fungi among different tissues, with Xylariales being the dominant fungi in rhizomes of and Hypocreales being the dominant fungi in the petioles, roots, and rhizomes of . Overall, the community similarity of endophytic fungi among locations is moderately dissimilar (26-50%), while the similarity between tissues is moderately similar (51-75%). The low diversity of endophytic fungi could be one of the main reasons for the endangerment of . The protection of the diversity of endophytic fungi in the underground parts of is essential for the conservation of this critically endangered mangrove fern.