Trichophyton rubrum is the most common agent of dermatophytosis, a disease that affects millions of individuals worldwide. Its molecular pathogenicity mechanisms are still not completely elucidated. It has been widely recognized that proteases secreted by T. rubrum are the key virulence factors during host infection. However, our knowledge about the expression of its secreted proteases in host infection is still obscure. This investigation provides the expression patterns and dynamics of secreted protease genes belonging to the subtilisins (SUB) and metalloproteases (MEP) gene families in T. rubrum. The data was obtained under simulated host infection conditions through relative quantification of real time PCR. Keratin, collagen, and elastin induced the expression of similar protease genes, and the expression patterns and dynamics of these protease genes in media containing human skin sections were different from those in media containing individual protein substrates. According to the expression dynamics of these protease genes, we conclude that Sub3, Sub4, and Mep4 may be the dominant proteases secreted by T. rubrum during host infection, and that these proteases could be good targets for new antifungal chemotherapy and molecular diagnostic markers. This work presents useful molecular details to further our understanding of the pathogenesis of dermatophytosis.