Protein kinases are key players in controlling many basic cellular processes in almost all the organisms via mediating signal transduction processes. In the present study, we characterized the cellulolytic Trichoderma reesei orthologs of Saccharomyces cerevisiae Sch9 and Yak1 by sequence alignment and functional analysis. The T. reesei Trsch9Δ and Tryak1Δ mutant strains displayed a decreased growth rate on different carbon sources and produced less conidia. The absence of these two kinases also resulted in different but abnormal polarized apical growth as well as sensitivity to various stresses. In addition, disruption of the genes Trsch9 or Tryak1 resulted in perturbation of cell wall integrity. Interestingly, while the induced production of cellulases was slightly compromised in the Trsch9Δ strain, the extracellular production of cellulases was significantly improved in the absence of Yak1. The results indicate that TrSch9 and TrYak1 play an important role in filamentous growth, stress response and induced production of cellulases in T. reesei.