The study presents data on the species composition of cyanobacterial water blooms in Czech fish ponds from the 1950s to the 1990s. Since the 1950s, a shift from large-colonial Aphanizomenon flos-aquae var. flos-aquae through Microcystis aeruginosa and small-colonial species of Anabaena to single-filament species (Planktohrix agardhii, Limnothrix redekei, Aphanizomenon gracile) or single-cell forms (Microcystis ichtyoblabe), has been observed. The changes in the species composition of the water blooms are closely related to changes in fishery management (increase in fish stock, increase in application of organic fertilizers). At present the high predation of fish upon zooplankton results in elimination of large colonial blooms of A. flos-aquae associated with large filtering zooplankton (Daphnia). Low grazing pressure of zooplankton, low light conditions and low N:P ratios are suitable conditions for mass development of the small species of cyanobacteria. High pH is not necessary to achieve cyanobacteria dominance.