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<i>Trichoderma</i> is known worldwide as biocontrol agents of plant diseases, producers of enzymes and antibiotics, and competitive contaminants of edible fungi. In this investigation of contaminated substrates of edible fungi from North China, 39 strains belonging to 10 <i>Trichoderma</i> species isolated from four kinds of edible fungi were obtained, and three novel species belonging to the Harzianum clade were isolated from the contaminated substrates of <i>Auricularia heimuer</i> and <i>Pholiota adipose</i>. They were recognized based on integrated studies of phenotypic features, culture characteristics, and molecular analyses of RNA polymerase II subunit B and translation elongation factor 1-α genes. <i>Trichoderma auriculariae</i> was strongly supported as a separate lineage and differed from <i>T. vermifimicola</i> due to its larger conidia. <i>Trichoderma miyunense</i> was closely related to <i>T. ganodermatigerum</i> but differed due to its smaller conidia and higher optimum mycelial growth temperature. As a separate lineage, <i>T. pholiotae</i> was distinct from <i>T. guizhouense</i> and <i>T. pseudoasiaticum</i> due to its higher optimum mycelial growth temperature and larger conidia. This study extends the understanding of <i>Trichoderma</i> spp. contaminating substrates of edible fungi and updates knowledge of species diversity in the group.