Mount Huangshan provides the habitat for a number of locally or nationally endemic plant species, several of which are globally threatened. Its outstandingly rich flora contains one-third of China's bryophytes (mosses and liverworts) and over half of its pteridophytes (ferns).

Species endemic to Huangshan include 13 species of pteridophytes and 6 species of higher plants, with many other species endemic to the region or to China.

This exceptional flora is complemented by an important vertebrate fauna of over 300 species, including 48 mammal species, 170 birds, 38 reptiles, 20 amphibians and 24 fish. A total of 13 species are under state protection, including the Clouded Leopard Neofelis nebulosa (VU) and the Oriental Stork Ciconia boyciana (EN).