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The presence of cyanobacteria in drinking water, aquatic foods and bathing water has created a significant major problem to global public health as these toxins induce damage in various organ including liver, cardiovascular, intestinal and central nervous systems. Although the morphologic, phylogenetic and toxicogenetic characteristics of cyanobacteria were identified in several lakes in China, many freshwater sources such as Dong Ting Lake, Hunan Province, China remain to be determined. Since the presence of these cyanobacteria may potentially affect human health, the aim of this study was to isolate, identify and characterize the most frequent occurring bloom-forming cyanobacteria in Dong Ting Lake, Hunan Province, China, which can provide information on the safety of utilization of this water source for drinking water, agriculture and recreation. Samples collected from the surface water of Dong Ting Lake were subjected to serial dilution in the lab for morphological analysis. Data demonstrated the morphological features were 2–5 µm diameters with rounded shapes and green color resembling Microcystis sp. The isolated cyanobacterial strain obtained from surface water samples in Dong Ting Lake was termed Microcystis sp. YFM2. The MC concentration was detected by enzyme-linked immunosorbent assay (ELISA) and found to be 92.88 µg/107 cells in Microcystis sp. YFM2. By polymerase chain reaction (PCR) results indicated that Microcystis sp. YFM2 isolated from Dong Ting Lake contained synthetase genes (mcyA-C). Our findings indicated that the dominant cyanobacteria Microcystis sp. YFM2 isolated from the freshwater Dong Ting Lake demonstrated morphologic, phylogenetic and toxicogenetic properties resembling a toxin generating cyanobacterium. Based upon this knowledge, it is essential to monitor the use of this Lake for future domestic, agricultural and recreational purposes. [ABSTRACT FROM AUTHOR]