Mangrove endophytic fungi can produce impressive quantities of metabolites with promising antioxidant activities that may be useful to humans as novel physiological agents. In this study, we investigated the phylogenetic diversity and antioxidant potential of 46 fungal endophytes derived from the mangrove species Rhizophora stylosa and R. mucronata from the South China Sea. The fungal isolates were identified using a combination of morphological characteristics and phylogenetic analysis of the internal transcribed spacer (ITS) sequences. Seventeen genera belonging to 8 taxonomic orders of Ascomycota were discovered, specifically, Botryosphaeriales, Capnodiales, Diaporthales, Eurotiales, Glomerellales, Hypocreales, Pleosporales, and Xylariales. The most abundant fungal orders included Xylariales (35.49%) and Diaporthales (27.61%), which were predominantly represented by the culturable species Pestalotiopsis sp. (34.54%) and Diaporthe sp. (18.62%). The stems showed more frequent colonization and species diversity than the roots, leaves, hypocotyls, and flower tissues of the host plant. The antioxidant activities of all the isolated fungal extracts on four different culture media were assessed using improved 2,2'-diphenyl-1-picrylhydrazyl (DPPH) and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonicacid) (ABTS) methods. A relatively high proportion (84.8%) of the isolates displayed antioxidant capacity (%RSA > 50%). Further research also provided the first evidence that HQD-6 could produce flufuran as a significant radical scavenger with IC50 values of 34.85±1.56 and 9.75±0.58 μg/mL, respectively. Our findings suggest that the utilization of a biotope such as that of the endophytic fungal community thriving on the mangrove plants R. stylosa and R. mucronata may be suitable for use as a sustainable resource for natural antioxidants.