Mitogen-activated protein (MAP) kinases modulate morphological and genetic processes, which determine cell fate. The tvk1 gene encodes a MAP kinase of Trichoderma virens and its deletion promotes an unusual conidiation phenotype in submerged culture. Here, it is reported that the morphology, physiology and expression of genes encoding cell wall proteins from Trichoderma are significantly affected by Tvk1. Morphological changes were evident in the cell walls of aerial conidia produced by a MAPK null mutant when compared to those produced by the wild-type. Unexpectedly, conidia produced in submerged culture by the Deltatvk1 strain were highly hydrophobic, whereas in aerial conidia hydrophobicity was severely reduced. In addition, the Deltatvk1 strain was unable to break the liquid-air interface when the fungus grew in rich medium; however, when it grew in minimal medium the fungus produced large filaments which were much more efficient at breaking the interface than the wild-type. Through cDNA subtractive hybridization between the wild-type and Deltatvk1 grown in submerged culture, five genes encoding hydrophobin-like proteins and two additional genes encoding cell wall proteins were identified. Four hydrophobin-encoding genes (Tv-hfb1, Tv-srh1, tv-cfth1 and Tv-qid3) and a gene encoding a clock-controlled-like protein (Tv-ccg14/TvSm1) were upregulated in Deltatvk1, whereas genes encoding a cell wall protein (tv-qid74) and an additional hydrophobin (tv-hfb3) were absent in the mutant strain. Clear differences in gene expression were shown during conidiation and emergence from the liquid-air interface, suggesting different functions of the corresponding proteins in these two phenomena. The results support a model in which Tvk1 regulates morphology and genes encoding cell wall proteins during development of Trichoderma.