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Microcystins (MCs) are commonly found in eutrophicated waterbodies such as lakes, ponds and reservoirs. MCs are hepatotoxins and create a high risk of liver tumors and cancer when MC-polluted water is drunk. Since MC-polluted waterbodies can form a normal part of many drinkiing water system, aggressive treatment to remove MC-LR type compounds has become an important issue worldwide. The objective of this study was to develop a method for the removal of high concentrations of MC-LRs (ppm level) by biodegradation using an indigious bacterial mixed culture isolated in Tawian. Using this culture-based biodegradation system, MC-LR removal of >99% is able to be achieved with the final concentration of MC-LR being measured to be 0.324 μg L −1 after 16 days. The pseudo -first rate constant of the MC-LR biodegradation was 876 μg L −1 day −1 during the first 4 days. The bacterial biodiversity during biodegradation was found to decrease during the first stage (Day 0–4) and then increased again during the second stage (Day 5–16), based on the Richness Index and Shannon-Wiener Diversity Index. The bacterial species identified in the mixed culture included Sphingomonas spp., Pseudoxanthomonas spp., Hyphomicrobium aestuarii , Sphingobium spp., Rhizobium spp., Steroidobacter spp. and Acinetobacter spp, all of which seem to. play important roles in MC-LR biodegradation. The genes mlrB and mlrC , which encodes proteins involved in various aspects of MC-LR biodegradation, were found to be present in the mixed cultures and are capable of being used as a biomarker for the MC-LR biodegradation process in Taiwanese reservoirs. [ABSTRACT FROM AUTHOR]