A novel bacterium capable of degrading two microcystin analogues, microcystin-LR and -LA (MCLR and MCLA), was isolated from a biological sand filter which was previously shown to effectively remove these toxins from source waters. Based on phylogenetic analysis of the 16S rRNA gene sequence, the isolated organism, LH21, most likely belonged to the genus Sphingopyxis and of the previously cultured species clustered with Sphingopyxis witflariensis. Using polymerase chain reaction (PCR), isolate LH21 was shown to contain homologues to each of the four genes, mlrA, mlrB, mlrC and mlrD previously associated with the degradation of MCLR by Sphingomonas sp. ACM-3962. Isolate LH21 was able to effectively degrade MCLR and MCLA in batch experiments under environmentally relevant conditions, with complete removal observed within 5h after re-exposure of the toxins.