A bacterium capable of degrading five microcystin (MC) variants, microcystin-LR, YR, LY, LW and LF at an initial total concentration of 50 μg l−1 in less than 16 hours was isolated from Missisquoi Bay, in the south of Quebec, Canada. Phylogenetic analysis of the 16S rRNA gene sequence identified the bacterium as Sphingopyxis sp., designated strain MB-E. It was shown that microcystin biodegradation activity was reduced at acidic and basic pH values. Even though no biodegradation occurred at pH values of 5.05 and 10.23, strain MB-E was able to degrade MCLR and MCYR at pH 9.12 and all five MCs variants tested at pH 6.1. Genomic sequencing revealed that strain MB-E contained the microcystin degrading gene cluster, including the mlrA, mlrB, mlrC and mlrD genes, and transcriptomic analysis demonstrated that all of these genes were induced during the degradation of MCLR alone or in the mixture of all five MCs. This novel transcriptomic analysis showed that the expression of the mlr gene cluster was similar for MCLR alone, or the mixture of MCs, and appeared to be related to the total concentration of substrate. The results suggested that the bacterium used the same pathway for the degradation of all MC variants.