As the rapid-changing in Trichoderma taxonomy, an efficient identification of Trichoderma species is an urgent issue for Trichoderma-based research. In this study, based on the current taxonomy of Trichoderma, we constructed curated databases including 338 ITS sequences, 435 TEF1 sequences, 415 RPB2 sequences and 28 phenotypic characters. In addition, a polyphasic identification system (PIST) was developed. Within PIST, the resolution ability of molecular and phenotype characters could be combined for species identification in a step-by-step way. Compared with other identification systems, the involved Trichoderma species were extended from 88 to 252 species and 175 from 188 tested Trichoderma species could be identified within PIST. In most tested cases, three nucleotide markers and phenotypic characters showed improved identification performance. The TEF1 sequences have superior resolution than other characters.
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