Abstract: Objective: To compare the accuracy and efficiency of two matrix-assisted laser desorption ionization time-of-flight mass spectrometry instruments(Autof ms 1000 and MALDI Biotyper) in identifying common clinical filamentous fungi. Methods: This study included 32 standard strains of filamentous fungi and 120 clinical isolates. The strains were identified using Autof ms 1000 and MALDI Biotyper according to standard operating procedures. The results were compared with sequencing molecular identification results. Results: At the species level, the Autof ms 1000 mass spectrometer detected 140 strains of filamentous fungi, with a detection accuracy rate of 92.1%(140/152). Among them, 126 strains had scores above 9.0, and 2 strains were misidentified, with a misidentification rate of 1.3%(2/152). The MALDI Biotyper mass spectrometer detected 98 strains, with a detection accuracy rate of 64.4%. There were 47 strains with scores above 2.0, only 3 strains had scores above 2.3, and 7strains were misidentified. Conclusion: Both the Autof ms 1000 and MALDI Biotyper mass spectrometry identification systems can be used for rapid identification of common filamentous pathogenic fungi in clinical practice,while the Autof ms 1000 mass spectrometer has more advantages.