Biogeography is flawed by a poor understanding of microbial distribution, due to the lack of systematical research framework, especially appropriate study units. We studied the biogeographic patterns of Nematode-Trapping Fungi by collecting and analyzing 2,250 specimens from 228 sites in Yunnan Province, China. We found typical watershed patterns both at the level of species and gene of Nematode-Trapping Fungi. The results showed that microbial biogeography could be better understood by 1) using watersheds as research units, 2) removing the coverup of widespread species, and 3) applying good sampling efforts and strategies. We suggest that watersheds could help unify the understanding of biogeographic patterns of animal, plant, and microbe, and may also help account for the historical and contemporary factors driving species distribution.