In the last decades, large number of reported cases of illnesses in Mozambique is related to drinking water. However, only a limited number of studies have focused on aquatic pollution in this country. Cyanobacterial blooms dominated by Microcystis sp are regularly identified in freshwater bodies in Mozambique. Microcystis is known to proliferate in freshwater bodies and produce microcystins which have adverse effects on animals and humans. The aim of this study was to quantify microcystinproducing Microcystis in three different freshwater bodies in Southern Mozambique. TaqMan based real time polymerase chain reaction (PCR) (Taq Nuclease Assay) was used to quantify populations of Microcystis in three aquatic ecosystems in Southern Mozambique. Total Microcystis spp (microcystinproducing and non-producing strains) were quantified in the three selected study areas with the determination of the copy numbers of the phycocyanin (PC) operon. Microcystin-producing gene copy numbers were quantified using specific primer pair, amplifying the mcyB gene. Microcystis mcyB copy numbers varied from 4.2 x 10 6 to 1.6 x 10 9 gene copies /L in 2008, corresponding to 2.15 to 98.55% of total Microcystis, and from 9.6 x 10 7 to 4.5