The present study was undertaken to explore the inhibitory effect of cyanobacterial extracts of Nostoc commune FA-103 against the tomato-wilt pathogen, Fusarium oxysporum f. sp. lycopersici. In an optimal medium, cell growth, antifungal activity, and antifungal compound production could be increased 2.7-fold, 4.1-fold, and 13.4-fold, respectively. A crude algal extract had a similar effect as mancozeb at the recommended dose, both in laboratory and pot tests. In vitro and in vivo fungal growth, spore sporulation and fungal infection of wilt pathogen in tomato seeds were significantly inhibited by cyanobacterial extracts. Nostoc commune FA-103 extracts have potential for the suppression of Fusarium oxysporum f. sp. lycopersici.