Objective To evaluate the capability of internal transcribed spacer (ITS) region sequencing analysis to identify clinical isolates of filamentous fungi.Methods A total of 267 filamentous fungi isolates collected from clinical specimens were analyzed by ITS region sequencing analysis.Alignment of acquired sequences with known sequences in GenBank and MycoBank was conducted to identify the species of those isolates.Results ITS sequences of the 267 isolates were amplified successfully.Among these isolates, 53.9％ (144/267) were identified to species level and 44.2％ (118/267) to genus level.Only five isolates were failed to be identified at genus level as they shared >95％ homology in ITS sequence with multiple genera.Conclusion ITS region sequencing analysis is preferred for identification of clinical isolates of filamentous fungi at genus level for its high universality and great capability.When species-level identification is required, some informative DNA markers besides ITS region should be included accordingly.