Tshipise, Mphephu and Sagole are thermal hot water springs in the Limpopo Province of South Africa with temperatures of 58, 43 and 45°C; and pH of 8.85, 8.08 and 9.70, respectively. The bacterial diversity of the hot water springs was determined by pyrosequencing of the two 16S rRNA hypervariable regions V1-3 and V4-7. Analyses of the community DNA revealed that bacterial populations as detectable by the V1-3 or V4-7 region, respectively were dominated by the Bacteriodetes and Proteobacteria for Mphephu, and Proteobacteria and Cyanobacteria for both Tshipise and Sagole. The major differences in the bacterial diversity between the springs was that no Cyanobacteria were detected for Mphephu and the level of Bacteriodetes detected for both Tshipise and Sagole was much lower compared to the levels detected at Mphephu. The Firmicutes were detected at all the springs but at a much lower abundance compared to the other main phyla detected. Various other phyla were detected at the hot springs at levels below 0.20% of the total sequences obtained. It is interesting that very diverse bacterial genera exist in the three hot water springs studied.