In the present study, the eutrophic level of 30 water samples collected from Lake hongze in August 2014 were analyzed, and the abundance of toxic and non-toxic Microcystis sp., together with their spatial distribution, was investigated by quantitative real-time PCR techniques. The results showed that the average concentrations of total nitrogen and total phosphorus were 1.63 and 0.11 mg x L(-1), respectively. The trophic state index ( TSI) ranged from 58.1 to 73.6, and the water quality was in the state of eutrophication based on TSI. Toxic Microcystis was widely distributed in Lake Hongze, and its abundance varied sharply, from 1. 13 x 10(4) to 3.51 x 10(6) copies x mL(-1), and the abundance of total Microcystis ranged from 1.06 x 10(5) to 1.10 x 10(7) copies x m(-1), meanwhile, the proportion of toxic Microcystis in the total Microcystis ranged from 8.5% to 38.5%, with the average value of 23.6%. Correlation analysis indicated that there was a significant positive correlation among total Mirocystis, toxic Microcystis and the toxic proportion (P < 0.01). The abundance of total and toxic Microcystis was significantly positively correlated to chlorophyll a ( Chl-a) concentrations and TSI (P < 0.01), but was negatively correlated to transparency (SD) (P < 0.01). The ratio of toxic Microcystis to total Microcystis was significantly positively correlated to Chl-a, TN, TP and TSI (P < 0.01), but significantly negatively correlated to the ratio of TN to TP and SD (P < 0.01). Therefore, reducing total nitrogen and phosphorus concentrations could not only lower the eutrophication level of Lake Hongze, but also inhibit the competition advantage of the toxic Microcystis over non-toxic Microcystis.