The luminescent microscopy (LM) is especially convenient for express analysis of the toxicity of various substances or for detecting the degree of inhibition of the physiological state of cyanobacteria populations as a result of the action of certain chemical compounds on them. In natural water bodies, the suppression of the development of the phytoplankton occurs, in particular, under the influence of low-molecular-weight organic compounds (LMWOCs), metabolites-allelochemicals, of aquatic macrophytes. LM, which allows observing the primary or secondary luminescence of microorganisms, was used by us to study changes in the physiological state of the cyanobacteria cultures of Synechocystis aquatilis and Aphanizomenon flos-aquae under the influence of allelochemicals of water macrophytes in laboratory experiments. We have shown (including using LM) that selected LMWOCs (linoleic, heptanoic, octanoic, tetradecanoic, hexadecanoic, and gallic acids) possess inhibitory allelopathic activity against cyanobacteria. However, their inhibitory effect was different. The highest values of the suppression index (SI > 10) were recorded (in ascending order) for hexadecanoic, linoleic, tetradecanoic, and gallic acids and a mixture of four allelochemicals (heptanoic, octanoic, tetradecanoic, and gallic acids). The creation of a new generation of algaecides/cyanocides based on LMWOCs of aquatic plants is a very promising strategy for combating "algal blooms."