Abstract: Trichoderma harzianum is one of the most common aggregate species of the genus. Based on different molecular characterizations, strains of T. harzianum have been divided into different subgroups, which has created confusion. We reexamined reference strains representing different subgroups under the name T. harzianum and its related species. Phylogenetic analysis using the NEIGHBOR program in the PHYLIP package based on ITS1 5.8S rDNA ITS2 sequence data distributed the tested strains among two phylogenetic groups (A and B), which was supported by high bootstrap values. Group A contains T. hamatum , T.asperellum, T. atroviride, T.koningii and T.viride , and is divided into two clades. T.viride is more closely related to T.koningii and T.atroviride than to T. hamatum and T. asperellum . Group B contains T. spirale , T. hamatum , T. inhamatum , T. harzianum and T. anam. Hypocrea vinosa , and is divided into six clades. T. inhamatum is further divided into two subgroups (Ti1 and Ti2), and T. harzianum comprises at least five subgroups(Th1, Th2, Th4, Th5 and Th6). The phylogenetic analysis of ITS1 5.8S rDNA ITS2 sequence also indicated the heterogeneity of T. hamatum ,since a neotype of T. hamatum is located in group A but other strains of T. hamatum are located in group B. The RAPD analysis of 18 strains representing T. harzianum and its related species coincided with phylogeny based on sequence analysis of the ITS regions.