Microalgae produce many secondary metabolites that are biologically active, including compounds that inhibit microbial growth. These could potentially function as biofungicides. The first selection criteria for potential strains suitable in the phytosanitary market is good in vitro inhibition of growth against specific phytopathogenic fungi and oomycetes and higher biomass productivity rates. In the present study, water extracts were prepared from 280 strains comprising of 33 Cyanophyceae strains (13 genera), 157 Chlorophyceae strains (29 genera), 80 Trebouxiophyceae strains (19 genera), 5 Klebsormidiophyceae strains (1 genus) and 1 Zygnematophyceae strain. These were tested in vitro against 6 phytopathogenic fungi and 3 phytopathogenic oomycetes. In total, 45% of the species had mycelial growth inhibitory activity against at least one pathogen. Cyanobacteria had the highest “hit-rate” (64%), followed by the Chlorophyceae (49%) and Trebouxiophyceae (30%). Water extracts of 19 strains had fungicidal and/or oomyceticidal activity – these were predominantly Cyanobacteria. The Cyanobacteria displayed a wider spectrum of inhibition with five strains being active against three or more phytopathogenic strains. Trichormis variabilis MACC-304 and Tolypothrix tenuis MACC-205 had inhibitory activity against 6 phytopathogens and Nostoc linckia MACC-612 inhibited 4 phytopathogenic strains. Each Chlorophyta strain was only active against 1-2 strains. However, the daily productivity rates of Cyanobacteria were significantly lower than Chlorophyta strains. Further investigation of 15 Nostocales species (Nostocaceae, Tolypothrichaceae and Calotrichaceae) showed the Nostoc species generally had significantly lower biomass generation compared to other Nostocacaeae strains. The most promising strain was Tolypothrix tenuis MACC-205 which had the most potent, broad spectrum fungal and oomyceticidal inhibitory activity as well as significantly higher daily biomass productivity rates. Thus, Cyanobacteria can potentially be developed as an effective agricultural tool for environmentally-friendly disease management.