The paper describes the isolation and characterization of a novel pelagic bacterial strain capable of hepatotoxic microcystin (MC) degradation. From a total of 24 bacterial strains isolated from water samples collected during the cyanobacteria blooming period in Jeziorsko reservoir, Poland, only the strain JEZ-8L was found to completely degrade microcystin-LR (MC-LR). The strain JEZ-8L was found to include the full mlrABCD gene cluster associated with the biological degradation of MC. To our knowledge, the strain JEZ-8L may represent the first report of an isolated bacterium to contain the full mlrABCD gene cluster in an aquatic ecosystem from central Europe. The nucleotide sequence analysis of each mlr gene and their translated amino acid sequences revealed a close similarity to other MC-degrading bacteria belonging to the Sphingomonadaceae family. Phylogenetic analysis using the bacterial gene marker 16S rRNA revealed 99% sequence similarity with nine strains from the Sphingosinicella genus. The nucleotide sequence similarity between the strain JEZ-8L and Sphingosinicella microcystinivorans Y2 was probably the most representative, since the strain Y2 is known to be a MC-degrading bacterium with confirmed detection from the full mlrABCD gene cluster. It is important to mention that our findings represent a preliminary study on the microbiota involved in MC degradation in water bodies from central Poland. The MC-degrading activity of the strain JEZ-8L could be promising for further research towards the elaboration of biotechnological solutions to reduce the harmful effects of MCs in water.