Climate changes result in a more and more frequently observed increase in the abundance of cyanobacteria in habitat. Still data is lacking on the effect of high concentrations of toxins on bacteria in peatbog ecosystems, including bacteriocenoses found in bladder traps of Utricularia vulgaris L. We have attempted to answer a question: how the substances produced by cyanobacteria affect the functional structure of their bacteriocenoses. An experiment was conducted under laboratory conditions with the aim to determine the effect of cyanobacterial toxins on the composition of bacteriocenoses of Utricularia vulgaris L. microbiome. Cyanobacteria metabolites, i.e., microcystin-LR and anatoxin-A, were analyzed in particular experimental variants. The study results demonstrated a significant impact of cyanobacteria metabolites on the qualitative and quantitative structure of bacteria colonizing catch traps of peatbog carnivorous plants. Taxonomic diversity and abundance of microorganisms were substantially higher in water than in catch traps. In peatland, the catch traps were densely populated by Acidobacteriae, Bryobacterales, Telmatospirillum and Bryobacteraceae. In carbonate fen the catch traps were densely populated by Acidobacteriae, Bacilli and Bryobacteraceae. However, the effects of cyanobacterial toxins differed depending on habitat type. Carbonate fen is a habitat of higher trophy; hence, eutrophication processes (including cyanobacteria blooms) may be more intensive. The present study is another step toward better understanding of critical transformations observed in peatbog ecosystems triggered by the changing climate, whereas future research should take account of the effect of cyanobacterial blooms on the remaining elements of the microbiome of the carnivorous peatbog plants.