Cyanobacteria are present in many drinking water reservoirs in the world, and some of them may produce microcystins, anatoxin-a and other natural toxins: In this study, two groups of algal toxins: microcystins and anatoxin-a, and associated toxin producers were investigated. Water samples from nine major drinking water reservoirs and seven associated water purification plants were collected. An HPLC and an LC/MS were employed to detect the concentrations of five microcystins (microcystins-LR, RR, YR, LW, LF) and anatoxin-a. Molecular biotechnology methods were used to sequence Microcystis sp. gene from the cyanobacteria bloom from two of the reservoirs. Monitoring results suggested that microcystins were present in all the drinking water reservoirs studied, and some of them had concentration higher than the WHO guideline of microcystins-LR (1 μg/L). Unlike microcystins, anatoxin-a was only found in four reservoirs, mostly in King-Men island. After comparing the DNA sequence with existing cyanobacteria reference database, Microcystis aeruginosa and other Microcystis sp. were confirmed present in the two reservoirs tested.