Cyanobacterial blooms can be harmful to environmental and human health due to the production of toxic secondary metabolites, known as cyanotoxins. Microcystins (MCs), one of the most widespread class of cyanotoxins in freshwater, have been found to be positively correlated with cyanobacterial biomass as well as with nitrogen and phosphorus concentrations in temperate lakes. However, in tropical water bodies, cyanobacterial density and cyanotoxin correlation to environmental factors is not fully understood. In the present study, we examined the effects of total nitrogen and total phosphorus (TP) concentrations among other environmental parameters on cyanobacterial community structure and MC concentrations in the Dau Tieng reservoir, a tropical, eutrophic water body in Southern Vietnam. Cyanobacterial biomass and MC content were monitored monthly from March 2012 to February 2013, when MCs were present in the Dau Tieng Reservoir. The highest concentrations of intracellular MCs were found in September and February when cyanobacteria biomass reached maximum values, with 2.50 and 2.13 μg MC.L–1 , respectively. Principle component analysis and redundancy analysis showed that MC concentration was positively correlated with the biomass of the cyanobacterial order Chroococcales, whereas TP was the primary abiotic factor influencing cyanobacterial biomass and MC concentrations in the Dau Tieng Reservoir. In addition, Bayesian model average analysis was used to construct a prediction model of MCs using cyanobacterial biomass and environmental variables revealing a suite of useful predictive factors for MCs in the Dau Tieng Reservoir, including water temperature, TP and the biomass of Chroococcales.