Geothermal water in Slovakia is because of its healing effects mainly used for recreational purposes. The aim of the diploma thesis is to find biodiversity of microorganisms in selected thermal springs of central Slovakia by the means of cultivation, microscopic and molecular methods (method MALDI – TOF MS). The research was focused on two thermal springs in Sklene Teplice, the thermal springs in Vyhne and Dudince. Furthermore, the quality of water samples from the springs was evaluated on the basis of selected physicochemical and microbiological indicators (according to Act Nr. 364/2004 Coll. and Directive 2000/60/EC). According to the Decree of the Ministry of Health of the SR Nr. 30/2002 Coll. the thermal waters from these springs were suitable for bathing. According to the Decree of the Ministry of Health of the SR Nr. 29/2002 Coll. no sample was suitable for drinking. Using the method MALDI – TOF MS, the species Lysinibacillus fusiformis and Pseudomonas monteilii were reliably identified in Sklene Teplice 1 and Acinetobacter pittii in Sklene Teplice 2. The species Acinetobacter baumannii, Enterococcus faecium and Pseudomonas putida were determined in Vyhne and the species Citrobacter freundii and Pseudomonas agarici in Dudince. In Sklene Teplice and Vyhne were identified species of filamentous iron bacteria, the species Leptothrix ochracea and Leptothrix pseudoochracea by using the microscopic method. The filamentous bacteria Aquaspirillum spp., Beggiatoa alba and Thiothrix sp. were determined in the water sample from Dudince. Different algae and cyanobacteria were also observed at delivery points. The species of filamentous cyanobacteria Phormidium splendidum was identified in all three localities.