In recent years, Macau Main Storage Reservoir (MSR) is experiencing a high level of cyanobacteria, particularly Microcystis spp. and C. raciborskii that can produce microcystin and cylindrospermposin, respectively. Long-time exposure to those cyanotoxins would affect the health of public, and thus reliable detection and quantification of the algae species are challenging in water quality management. The traditional manual counting is mainly involving microscopic identification and counting of cells, which are limited by inaccuracy and time-consuming. As development of molecular techniques and increasing number of microbial sequences available in the Genbank database, the use of molecular methods can be used for more rapid, reliable and accurate detection and quantification. In this study, polymerase chain reactor (PCR) and real-time quantitative PCR (qPCR) techniques were developed and optimized. The results showed that the techniques were successful for identifying and quantifying the species in pure cultures and mixed cultures, and were proved to be potential application to water samples in MSR. Similar cells numbers estimated by microscopic counting and qPCR were obtained, when the target species exceeded approximately 1 million cells/L. The molecular approaches provide another reliable monitoring option, in addition to the traditional microscopic counting, for drinking water monitoring program.