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Bacterial strain 4B4 capable of degrading microcystin-LR (MC-LR) was isolated from the Beira Lake (N 6° 55’ 46’’, E 79° 51’ 15’’) in Sri Lanka. Based on phylogenetic analysis of the 16S rRNA gene sequence, the isolate 4B4 was identified as Stenotrophomonas maltophilia. The bacterium showed 100 % removal of MC-LR in 10 and 8 days of incubation at 28 °C and 32 °C, respectively. Optimisation studies confirmed that the addition of nitrates (0.4 ppm) and phosphates (0.02 ppm) to the medium can increase the microcystin removal rate of the bacterial strain. Further evaluation of S. maltophilia revealed that it is capable of degrading other microcystin analogues; microcystin-RR, -LW, -LF and nodularin (NOD) as well.