Wood-decaying fungi decompose the cellulose, hemicellulose and lignin of wood by producing various hydrolytic enzymes, and therefore play a key ecological role in the nutrient cycle of forest ecosystems. In August 2016, a survey of wood-decaying fungi was carried out in Gutianshan National Nature Reserve, Zhejiang Province. Fungal species were identified using morphological characters and DNA sequence analysis. Both the species composition and biogeography were also analyzed. A total of 92 fungal species, 78 white rot species and 14 brown rot species, representing 45 genera were identified from the 158 samples collected. Among these fungi, tropically-contained families are better represented than cosmopolitan families. Of the 158 specimens, 97 (76 species) were collected from woody substrates with a diameter larger than 10 cm, 48 (38 species) from a dead branch with a diameter ranging from 2 cm to 10 cm, and 13 (12 species) from a dead twig with a diameter smaller than 2 cm. The abundance of fungal species differed conspicuously in different decaying classes of dead wood as well. Of 92 fungal species, seven species (nine specimens) were collected from woody substrate of decay class 1, 45 species (86 specimens) from wood of decay class 2, 29 species (49 specimens) from wood of decay class 3, and 14 species (14 specimens) from wood of decay class 4. This study indicates that the diameter and decay class of dead wood are important factors influencing the growth and species distribution of wood-decaying fungi.