World-wide appreciated strategy for the management and treatment of high level and long lived radioactive waste is to dispose it in a deep and stable geological formation. Microbial community present in the host or buffer material may compromise the effective performance and safety of waste disposal system. In the Czech Republic, bentonite from Černý vrch locality is planned to be used as a buffer material. Therefore, microbial community was analysed in two bentonite samples (homogenized and raw bentonite) from this source.16S rRNA gene was amplified targeting the variable V4 region and sequencing was performed using Ion Torrent platform. Both bentonite samples were inhabited by relatively similar bacteria. Beta and Alpha-proteobacteria dominated both samples. Moreover, chemolithotrophs including Thiobacillus, Gallionella and Nitrosomonas capable of oxidising NH3, Mn2+, Fe2+ and S2- were also present.