Two new species of Trichoderma are described based on the collections producing ascomata or asexual morphs on woody substrates, and named as Trichoderma fujianense and T. zonatum. Trichoderma fujianense produces gliocladium to verticillium-like conidiophores, slender to lageniform phialides, green and ellipsoidal to cylindrical conidia. Trichoderma zonatum is characterized by pulvinate, pale yellow to light brown stromata with densely disposed dark green to black ostioles, monomorphic ascospores, simple trichoderma-like conidiophores, green, (sub)globose to pyriform conidia. Their phylogenetic positions were investigated inferred from sequence analyses of the combined RNA polymerase II subunit b and translation elongation factor 1-α genes. The results indicate that T. fujianense, along with T. aureoviride and T. candidum, represents an independent lineage with high statistical support. Trichoderma zonatum belongs to the Chlorosporum clade and is associated with but clearly separated from T. rosulatum and T. costaricense. Morphological distinctions and sequence divergences between the new species and their close relatives were discussed.