Fungi in marine ecosystems occurred as parasites or symbionts of other marine organisms and as decomposers, which play ecological importance. Fungal diversity in the sediment of intertidal region is poorly understood. Using ribosomal RNA internal transcribed spacer-2 (ITS2) metabacording, we investigated the distribution patterns of fungal communities in sediment of Chinese intertidal zone. Our data revealed a high level of fungal diversity in this special region, as represented by 6013 OTUs that span six phyla, 23 classes, 84 orders and 526 genera. Majority of them are traditionally known as terrestrial fungi (e.g. Aspergillus, Cladosporium, Penicillium, Gibberella, Taifanglania, Talaromyces). Obligate marine fungi (e.g. Corollospora, Lignincola, Remispora, Sigmoidea) also occurred with small proportion, as well as the fungal basal linages including Chytridiomycota, Zygomycota, and Rozellomycota. Ninety-nine species represented by 101 OTUs were annotated and eight of them (e.g. Aspergillus tritici, Bionectria epichloe, Exophiala xenobiotic) appeared to be extremely common and occurred in more than half of all samples. Both OTU richness and community compositions in intertidal sediment of different seas were found to vary, indicating a significantly spatial variation of fungal diversity. However, no significant difference in community compositions was detected between most habitat types, with exception of plant habitat where specific groups (e.g. mangrove fungi) occurred. Our data also suggested that human activities might profoundly affect compositions of fungal community along Chinese intertidal regions.