Flaxseed cyclolinopeptides (FCLPs) were cyclic peptides extracted from flaxseed. Their bioactivities were not elucidated yet. To evaluate antifungal activity of these FCLPs, two strains, Paecilomyces varioti bainier （AS 3.776）and Aspergillus flavus （CICC 2476）, were selected as test strains and inoculated on potato dextrose agar (PDA) with FCLPs of serial concentrations added before or after autoclave. Radial growth, spores formation and spores germination were measured. Results showed that half-inhibition concentration (IC₅₀) on spores formation of FCLPs mixtures against Paecilomyces varioti bainier were 0.53 mg/mL (autoclaved) and 0.34 mg/mL (not autoclaved), against Aspergillus flavus were 0.31 mg/mL(autoclaved) and 0.24 mg/mL (not autoclaved) respectively. Antifungal activity of FCLPs were found mostly retained after autoclave. Residual antifungal activity against Paecilomyces varioti bainier were found as much as 76.8% (radial growth) and 76.7% ( spores formation), gainst Aspergillus flavus 61.6% (radial growth) and 41.7% ( spores formation) respectively. Results of spores germination test indicated that the average inhibition rate against Paecilomyces varioti bainier (17.8%) was higher than that against Aspergillus flavus (7.8%). After fungi culture, FCLPs were extracted from PDA and analyzed by high performance liquid chromatography (HPLC). Results indicated that autoclave decreased the content of FCLPs in the media. This may lead to the decrease of antifungal activity. In this study, FCLPs were found to have antifungal activity. And the activity partially remained after autoclave. It is indicated that FCLPs have the advantages over current antimicrobial peptides when applied in food processing involved with heat treatment