Objective:To establish a method of sequencing of internal transcribed spacer 2 (ITS2) for identification of filamentous fungi from clinical specimens. Methods:Amplification and sequencing of internal transcribed spacer 2 (ITS2) region of fungi were performed using universal primers. Searches of current nucleotide databases in GenBank were carried out with the BLAST algorithm. Results:9 clinical common fungal isolates were accurately identified . 6 clinical filamentous fungi isolates were detected. Conclusions:ITS2 sequencing for ilamentous fungi is an excellent method.