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The increasing production of microcystin-LR (MC-LR) causing animal and human health issues is found in eutrophic water bodies, marine habitats and desert environments. The health threat posed by MC-LR has led to the establishment of World Health Organization's water guideline value of 1 μg/mL. Combating this has increased the search for cost-effective approach to degrade MC-LR. The study aimed to optimize the MC-degrading environmental factors of bacterial community YFMCD4. Response surface methodology (RSM) was employed to evaluate the influence of varying temperatures, pH and initial MC-LR concentration on the biodegradation efficiency of MC-LR by bacterial community YFMCD4. The optimal MC-LR biodegradation environmental factors were found to be 30 °C, pH 7 and 2 μg/mL initial MC-LR. The biodegradation rate reached 100% after 10 h. YFMCD4 mainly consisted of genera Alacligenes , Sphingobacterium and Pseudomonas using High-throughput pyrosequencing technology. The mlrA gene encoding MlrA enzyme considered most important for MC-LR biodegradation was obtained from YFMCD4. Data demonstrated that the bacterial structure and biodegradation efficiency of YFMCD4 varied with the change of environmental factors including temperature, pH and MC-LR concentrations. RSM is considered a good method to examine the optimal biodegradation environmental conditions for MC-LR. To date, RSM and High-throughput pyrosequencing technology are employed to optimize the biodegradation conditions (30 °C, pH 7 and 2 μg/mL initial MC-LR) and analyze the structure of bacterial community for the first time. • RSM was used to optimize MC-LR biodegradation conditions by YFMCD4 for the first time. • Varying temperatures, pH and MC-LR concentrations influenced MC-LR biodegradation. • Structure of YFMCD4 was analyzed by high-throughput pyrosequencing technology. • mlrA and mlrD homologues genes were amplified from YFMCD4. [ABSTRACT FROM AUTHOR]