MESHWR / Department of Ecology and Resources Management / The presence of harmful algal blooms (HABs) and cyanobacteria toxins in drinking water sources are known to pose a great threat to humans. The main aim of this study was to use molecular technique to determine the origins of the cyanobacteria species at Musina raw water abstraction point by identifying and comparing the non-toxic and toxic cyanobacteria species in the Limpopo River and some of its tributaries based on the phylogenetic analyses of 16S rRNA gene. The Musina water treatment plant is located downstream of a weir and the Beit bridge on the Limpopo River and the raw water supply is abstracted from 22 boreholes of which 14 are along the Limpopo River and 8 boreholes are inside the Limpopo River channel. The bottom sediments samples were collected from these rivers: Limpopo, Crocodile, Mokolo, Mogalakwena, Nzhelele, Lephalale, Sand rivers (South Africa); Notwane (Botswana), Shashe River and Mzingwane River (Zimbabwe). The physical-chemical analysis of the bottom sediments showed the availability of nutrients, nitrates and phosphates, in excess of 0.5 mg/l for most the of rivers, alkaline pH and salinity in excess of 500 mg/l. Total genomic DNA were extracted from cyanobacteria species on the bottom sediments and Polymerase Chain Reaction (PCR) method was used to detect the genetic profile of the cyanobacteria species. Molecular identification of cyanobacteria was based on PCR amplification and sequencing of the 16S rRNA gene. The 16S rRNA gene was absent from sediments of the Mogalakwena and Lephalale rivers but present in all other selected rivers. The cyanotoxins detection was also based on PCR by amplification of microcystin/nodularin and cylindrospermopsin polyketide synthetase genes. Most of the samples showed no amplification of the toxin genes. While two samples showed the amplification of cylindrospermopsin polyketide synthetase gene (Sand River and Nzhelele River Next to Tshipise) and two samples showed amplification for microcystin/nodularin synthetase gene, Crocodile River and Mzingwane River. The first was the confirmation of similarity of samples from Crocodile River downstream of hartbeespoort Dam and Shashe River to Leptolyngbya boryana with 99% bootstrap confidence. The similarity of sample from Musina borehole to Sand River upstream to Alkalinema pantanalense with 98% bootstrap. Thus, the presence of toxic genes may imply the presence of toxic cyanobacteria species in the river sediments and may be hazardous to humans because rural communities and commercial farmers abstract water from Limpopo River catchment for human consumption, livestock and irrigation. The waters of the Limpopo River basin also provide drinking water to wildlife and a habitant for aquatic organisms/animals.