Macrofungi not only play an important role in pollution control and other environmental protection measures, but also an important resource in food and pharmaceutical industries. However, the diversity of the macrofungal community in the core habitat of the giant panda in Bifeng Gorge, China is still inadequate. In the current study, the macrofungal diversity in Bifeng Gorge was investigated using morphologic and molecular biological methods. The results show that 275 species were found which were classified into 122 genera from 52 families. Up to 54.55% of the species were classified into various families, including Russulaceae, Strophariaceae, Agaricacea, Tricholomataceae, Psathyrellaceae, Mycenaceae, Marasmiaceae and Polyporaceae. The microfungi thrive in different areas within the Bifeng Gorge, which could be roughly classified into six ecological communities, namely, evergreen broadleaf forest (I), Cryptomeria fortunei forest (II), Metasequoia glyptostroboides forest (III), bamboo forest (IV), mixed bamboo-broadleaf forest (V) and grassland (VI). Further studies revealed that the order of the richness index (R) was I > II > V > III > IV > VI, evenness index (E) and dominance index (D) were V > III > IV > I > II > VI, and species diversity index (H') was I > V > III > IV > II > VI. The data suggests that despite the lagged sporophore peak compared with the highest temperature, macrofungal diversity was positively related to the temperature in the area.