Nematophagous fungi are an important group of soil microoganisms, which serve as natural enemies of nematodes and play important roles in maintaining nematode population dynamics in natural environments. Nematophagous fungi can attack and kill nematodes through producing specialized capturing devices, or toxins. Serine proteases are important virulence factors involved in the pathogenicity of nematophagous fungi infect against nematodes. Recently, pathogenicity-related serine proteases from different nematophagous fungi have been extensively characterized, especially, greater progress have been made in their crystal structure and molecular evolution. Here, the biochemical properties and functions of the pathogenicity-related serine proteases in nematophagous fungi were summarized, and the latest progress about their crystal structure, catalytic mechanism and molecular evolution were reviewed.