Casuarina equisetifolia forests are widely spread in tropical to subtropical coast, serving as windbreak forests. However, C. equisetifolia forests have poor natural regeneration rate, which were considered involving the allelopathy of the litter. The aim of the study was to investigate the characteristics of endophytic and epiphytic fungal communities of the litter in C. equisetifolia forests (young-aged forest, middle-aged forest and mature-aged forest) at Guilinyang coast of Haikou, Hainan province, China. The ITS rDNA was sequenced by Illumina high-throughput sequencing technology, which was used to analyze the diversity of the microbial communities of the litter from different aged forests. The litter and soil physicochemical properties were measured to determine the correlations between them. A total of 669,476 valid sequences were obtained for all samples and contained 6 phyla, 23 classes, 59 orders, 119 families, 212 genus, and 314 species. The diversity and abundance of the epiphytic fungal communities of the C. equisetifolia litter was higher than those of the endophytic fungi. There were greater similarity among the endophytic and epiphytic fungal community compositions. It was found that Ascomycota and Basidiomycota were the main fungi of the litter. There were three dominant orders exist in both endophytic and epiphytic fungal communities, including Capnodiales, Xylariales and Auriculariales. Coniochaetales, Magnaporthales and another two orders were specially distributed in the litter, while Basidiobolales and Trichosporonales were endemic to epiphytic fungi. The pH and organic carbon of the litter were significantly correlated to endophytic fungal community structure, while the bulk density and ammonium nitrogen of the soil were significantly correlated to epiphytic fungal community structure. This work provided an important theoretical basis for studying the role of microorganisms in the decomposition of C. equisetifolia litter.