Abstract:[Background] Microcystins (MCs), one of the main harmful substances produced by cyanobacterial bloom, are found in estuaries, lakes and coastal waters. [Objective] Under different concentrations of carbon, nitrogen and phosphorus sources, the paper analysed the ability of Novosphingobium sp. ERN07 to remove MCs so as to achieve rapid degradation of MCs. [Methods] The degradation characteristics were determined by orthogonal experiments and gene transcription analysis associated biodegradation with the expression of functional genes so as to understand the degradation mechanism. [Results] The dual nutrients composed of glucose and sodium nitrate had weaker inhibition of biodegradation than single glucose or sodium nitrate. Compared to those under standard MSM medium, the decelerated biodegradation with glucose or sodium nitrate (1 000 mg/L) or phosphorus source (500 mg/L) related to lower up-regulation in mlr gene expression, suggesting that divergent mlr gene expression was one of the reasons influencing various nutrient conditions on degradation. [Conclusion] Novosphingobium sp. ERN07 has a high degradation ability of MCs. Before the bloom, carbon and nitrogen sources were removed effectively so that it can be effectively used in MCs polluted water treatment.