To evaluate antifungal activity of these flaxseed cyclolinopeptides, 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. IC50 of FCLPs mixtures on spores formation of P. varioti bainier were 0.53 mg/mL (autoclaved) and 0.34 mg/mL (not autoclaved), and IC50 on A. flavuswere were 0.31 mg/mL (autoclaved) and 0.24 mg/mL (not autoclaved), respectively. Most of antifungal activity of FCLPs was retained after autoclave. Residual antifungal activity against Paecilomyces varioti bainier were found as much as 76.8% (radial growth) and 76.7% (spores formation) of original activity, and those gainst A. flavus were as much as 61.6% (radial growth) and 41.7% ( spores formation), respectively. Results of spores germination test indicated that the average inhibition rate against P. varioti bainier (17.8%) was higher than that against A. flavus(7.8%). After fungi culture, FCLPs were extracted from PDA and analyzed by high performance liquid chromatography (HPLC). Results indicated that the content of FCLPs in the media was decreased due to autoclave and thus led 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 had the advantages over current antimicrobial peptides applied in food processing involved with heat treatment。