The application of cyanobacteria metabolites in agriculture is considered a promising alternative to chemical fungicide because they are rich in many bioactive metabolites. Antifungal potentiality of Desertifilum tharense PS 11 extracts with different solvents was tested in vitro against Fusarium oxysporum f. sp. lycopersici. The D. tharense PS 11 methanol extract showed the highest antifungal activity against F. oxysporum (19.11%). Then, it was analyzed by GC-MS and LC-ESI-MSto identify and quantify its bioactive compounds. GC-MS and LC-ESI-MS analysis of D. tharense methanol extract investigate that the extract was rich in several metabolites such as phenols, alkanes amino acids, peptides, flavonoids, fatty acids and phthalic acid derivatives. After that, pot experiment was performed to test the efficiency of D. tharense PS11 methanol extract in the control of tomato vascular wilt disease caused by F. oxysporum f. sp < em>. lycopersici and growth promotion activity. Correspondingly, the results indicate a 50% reduction in disease incidence. Furthermore, D. tharense methanol extract exhibited a significant effect on plant growth and tomato yield. Therefore, this study clearly demonstrated that methanol extract from D. tharense PS 11 is a promising biochemical control agent against F. oxysporum f. sp < em>. lycopersici and can enhance tomato growth.