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Cyanobacterial blooms (HCBs) in water bodies adversely affect aquatic ecosystems. In laboratory experiments, metabolites-allelochemicals of aquatic macrophytes, nonanoic – a monobasic saturated and palmitoleic – an Omega-7 monounsaturated fatty acids effectively inhibit the development of cyanobacteria Synechocystis aquatilis Sauvageau, strain No. 1336 of CALU (Collection of Algae of Leningrad University). In contrast to palmitoleic acid (Suppression Index (SI) within 3.5), nonanoic acid at the highest tested concentrations of 1–1.8 mg/l (SI above 20) had more pronounced effect. Nonanoic acid can be referred to an algaecide of a new generation based on aquatic macrophyte metabolites to prevent and attenuate HCBs.