▶ Microcystis spp. was the main toxin producer in Kranji Reservoir. ▶ High temperature, light and nutrient led to high, constant Microcystis population. ▶ Toxic cell percentage was higher than studies in subtropical and temperate regions. ▶ Microcystis population was controlled by the availability of nutrient. The temporal variations in cyanobacteria and microcystin production in a tropical reservoir, Kranji Reservoir in Singapore, were studied from February 2008 to August 2009 by using molecular techniques and enzyme-linked immunosorbent assay (ELISA) respectively. Results from PCR and qPCR showed that Microcystis and Anabaena were present (mean concentrations 4.16 × 10 6 gene copies/mL and 4.47 × 10 4 gene copies/mL respectively) and were well correlated to each other ( P < 0.001) but that Microcystis was the primary microcystin producer. The average percentage of toxigenic Microcystis spp. was 55.92%, whereas no Anabaena-specific microcystin producing gene was detected. Microcystis-specific microcystin-producing genes mcyB and mcyD were detected in all the samples, together with dominant detection of mcyA and mcyE genes. However, a low positive detection rate was observed for mcyC. Due to the combined effects of high temperature, light and nutrient conditions in this tropical reservoir, the Microcystis cell concentrations were higher and more uniform compared to other Microcystis blooms reported in subtropical and temperate regions. Furthermore, the proportion of toxigenic Microcystis in the total Microcystis population was considerably higher. Principle component analysis and multiple linear regression analysis showed that total nitrogen and total phosphorus were positively correlated with the abundances of total Microcystis and toxigenic Microcystis. In addition, total nitrogen, pH and dissolved oxygen were positively correlated with the microcystin concentration.