Microcystins are cyclic heptapeptide toxins produced by cyanobacteria. They are potentially a threat to human and domestic animals so are of worldwide interest. Microcystin-LR is stable in various environmental conditions. It is important to know the factors affecting microcystin degradation which can be utilised in water treatment methods. This research is focused on activity of indigenous microflora in biolog MT2 plates and use of active isolates for degradation study. The growth and degradation patterns were compared with the known microcystin-LR degrading bacteria Paucibacter toxinivorans (DSMZ-16998) as a positive control. A total of 18 bacteria were isolated from three different sources and screened for the degradation study. Individual isolates and P. toxinivorans were exposed to microcystin-LR in a range of different media namely, physiological saline, R2A medium, nutrient broth and water at different concentrations of 0.50 1g/ml and 10.00 1g/ml of microcystin-LR. Degradation of microcystin-LR content was analysed by HPLC. Bacteria in mixed culture i.e. natural water samples were able to degrade microcystin-LR in low concentration within a week but were unable to degrade in high concentration until 30 days at room temperature. Degradation of microcystin-LR by cell extract of active isolates and P. toxinivorans was observed. Percentage loss of microcystin content by enzymatic degradation was observed from 22-42 percent in tested samples.